Package: a4 Version: 1.32.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo License: GPL-3 MD5sum: 00e7562c4412f2a31b54919b66137388 NeedsCompilation: no Package: a4Base Version: 1.32.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 077a2873fd1bea468bc86307a1eee4e7 NeedsCompilation: no Package: a4Classif Version: 1.32.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 MD5sum: c194b90cc4d80c9d589d6c1269ac4da2 NeedsCompilation: no Package: a4Core Version: 1.32.0 Depends: methods, Biobase, glmnet License: GPL-3 MD5sum: 0764afbd62979e811eaf99fda4807e15 NeedsCompilation: no Package: a4Preproc Version: 1.32.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: f28197ecba4a5696660442d33aa6638d NeedsCompilation: no Package: a4Reporting Version: 1.32.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 MD5sum: c37278b81f6909876a48043145cbdacc NeedsCompilation: no Package: ABAEnrichment Version: 1.14.1 Depends: R (>= 3.4) Imports: Rcpp (>= 0.11.5), gplots (>= 2.14.2), gtools (>= 3.5.0), ABAData (>= 0.99.2), data.table (>= 1.10.4), GOfuncR (>= 1.1.2), grDevices, stats, graphics, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: d73c75db7acac124dbc36a734d4d71fe NeedsCompilation: yes Package: ABarray Version: 1.52.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: 549b89684d9e319caac557f517acc7e3 NeedsCompilation: no Package: abseqR Version: 1.2.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: a1cf442849ec89bc9937730094727705 NeedsCompilation: no Package: ABSSeq Version: 1.38.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: 3b22e021c165c711734201fe2d8c9503 NeedsCompilation: no Package: acde Version: 1.14.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: 5bca02d14050dab364619ac2f3fc1dd0 NeedsCompilation: no Package: ACE Version: 1.2.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 6190b52169f64b8372c05c2c920a2e55 NeedsCompilation: no Package: aCGH Version: 1.62.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 MD5sum: be0bef86c5af1ecdb9c23f26dcea7595 NeedsCompilation: yes Package: ACME Version: 2.40.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: graphics, stats License: GPL (>= 2) MD5sum: dda3b6d9d427487387d71d30ec8ac676 NeedsCompilation: yes Package: ADaCGH2 Version: 2.24.0 Depends: R (>= 3.2.0), parallel, ff, GLAD Imports: bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH, snapCGH Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) MD5sum: 61c8ba54a1304c9c18fc0d47b8d75dae NeedsCompilation: yes Package: ADAM Version: 1.0.0 Depends: R(>= 3.5), stats, utils, methods Imports: Rcpp (>= 0.12.18), GO.db (>= 3.6.0), KEGGREST (>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment (>= 1.10.1) LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 7d35a54f2e960ec7a7ec8f6f8f9a2e54 NeedsCompilation: yes Package: ADAMgui Version: 1.0.0 Depends: R(>= 3.6), stats, utils, methods, ADAM Imports: GO.db (>= 3.5.0), dplyr (>= 0.7.6), shiny (>= 1.1.0), stringr (>= 1.3.1), stringi (>= 1.2.4), varhandle (>= 2.0.3), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), ggpubr (>= 0.1.8), ggsignif (>= 0.4.0), reshape2 (>= 1.4.3), RColorBrewer (>= 1.1-2), colorRamps (>= 2.3), DT (>= 0.4), data.table (>= 1.11.4), gridExtra (>= 2.3), shinyjs (>= 1.0), knitr, testthat Suggests: BiocStyle License: GPL (>= 2) MD5sum: 1c158e0c42e546c9f3eba19fb76a486a NeedsCompilation: no Package: adaptest Version: 1.4.0 Depends: R (>= 3.5.0) Imports: origami (>= 1.0.0), tmle, calibrate, methods, graphics, stats, utils, SummarizedExperiment Suggests: testthat, Matrix, SuperLearner, earth, gam, nnls, airway, rmarkdown, knitr, BiocStyle License: GPL-2 MD5sum: 01ac7bda196917f184b581d772f2b112 NeedsCompilation: no Package: adductomicsR Version: 1.0.0 Depends: R (>= 3.6), adductData, ExperimentHub, AnnotationHub Imports: parallel (>= 3.3.2), data.table (>= 1.10.4), OrgMassSpecR (>= 0.4.6), foreach (>= 1.4.3), mzR (>= 2.14.0), ade4 (>= 1.7.6), rvest (>= 0.3.2), pastecs (>= 1.3.18), reshape2 (>= 1.4.2), pracma (>= 2.0.4), DT (>= 0.2), fpc (>= 2.1.10), doSNOW (>= 1.0.14), fastcluster (>= 1.1.22), RcppEigen (>= 0.3.3.3.0), bootstrap (>= 2017.2), smoother (>= 1.1), dplyr (>= 0.7.5), zoo (>= 1.8), stats (>= 3.5.0), utils (>= 3.5.0), graphics (>= 3.5.0), grDevices (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat License: Artistic-2.0 MD5sum: f46d8533250c8bb1e9c5c85409c1b96d NeedsCompilation: no Package: adSplit Version: 1.54.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods, multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) MD5sum: a392edf9d83df7654bce88050c3d9a61 NeedsCompilation: yes Package: AffiXcan Version: 1.2.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 1ecf671ff853da1943fa93927c9a84d9 NeedsCompilation: no Package: affxparser Version: 1.56.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 27535bccec824509ea79df83a641e32d NeedsCompilation: yes Package: affy Version: 1.62.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) MD5sum: 0eb552db00c271587a6736744dfa0218 NeedsCompilation: yes Package: affycomp Version: 1.60.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: 2e6ae6a236b15e9d2fd7f376611e4841 NeedsCompilation: no Package: AffyCompatible Version: 1.44.0 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 MD5sum: 997af0dcfd3582138684f9d81580588b NeedsCompilation: no Package: affyContam Version: 1.42.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata Suggests: hgu95av2cdf License: Artistic-2.0 MD5sum: 39f0ab0f6b0ae300d20a01ff7bb67a55 NeedsCompilation: no Package: affycoretools Version: 1.56.0 Depends: Biobase, methods Imports: affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown License: Artistic-2.0 MD5sum: ce4c6af2de95858a0223ca0fc00c0fca NeedsCompilation: no Package: AffyExpress Version: 1.50.0 Depends: R (>= 2.10), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL MD5sum: 428dc21416445e4ca92bbe44502f26a7 NeedsCompilation: no Package: affyILM Version: 1.36.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, Biobase Suggests: AffymetrixDataTestFiles, hgfocusprobe License: GPL-3 MD5sum: 1d882d602cf45f48b6ccec53d761dc31 NeedsCompilation: no Package: affyio Version: 1.54.0 Depends: R (>= 2.6.0) Imports: zlibbioc, methods License: LGPL (>= 2) MD5sum: 4a115565876093c68f17dc28c9274592 NeedsCompilation: yes Package: affylmGUI Version: 1.58.0 Imports: grDevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyPLM, gcrma, BiocGenerics, BiocManager, R2HTML, xtable License: GPL (>= 2) MD5sum: 6cf0ca5e075473d5e96e59febe8f630c NeedsCompilation: no Package: affyPara Version: 1.44.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1), affyio Suggests: affydata Enhances: affy License: GPL-3 MD5sum: 0b8f11ce29ec0e877c3b010974975502 NeedsCompilation: no Package: affypdnn Version: 1.58.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL MD5sum: 3bdf72549b4a89495ee30df5b025338f NeedsCompilation: no Package: affyPLM Version: 1.60.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0), Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, graphics, grDevices, methods LinkingTo: preprocessCore Suggests: affydata, MASS License: GPL (>= 2) MD5sum: 8070d4cba459fb7998c26c3d7c0ed571 NeedsCompilation: yes Package: affyQCReport Version: 1.62.0 Depends: Biobase (>= 1.13.16), affy, lattice Imports: affy, affyPLM, Biobase, genefilter, graphics, grDevices, lattice, RColorBrewer, simpleaffy, stats, utils, xtable Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) License: LGPL (>= 2) MD5sum: de5e5962fb74cd0b4deed0ebc0898b88 NeedsCompilation: no Package: AffyRNADegradation Version: 1.30.0 Depends: R (>= 2.9.0), methods, affy Suggests: AmpAffyExample License: GPL-2 MD5sum: bd6cf71aecceb26a25b7b6b8a4e651a1 NeedsCompilation: no Package: AGDEX Version: 1.32.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: eef4f67c480d45fa194afd886da71abc NeedsCompilation: no Package: agilp Version: 3.16.0 Depends: R (>= 2.14.0) License: GPL-3 MD5sum: 1445a40d1bf7d80b5c2b32b093dac65b NeedsCompilation: no Package: AgiMicroRna Version: 2.34.0 Depends: R (>= 2.10),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 MD5sum: 4a07273782f1b205dddbb221aeae7c7c NeedsCompilation: no Package: AIMS Version: 1.16.0 Depends: R (>= 2.10), e1071, Biobase Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: bd6fd76b022c0aeaeadc06cfe332a09a NeedsCompilation: no Package: ALDEx2 Version: 1.16.0 Depends: methods, stats Imports: BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest Suggests: testthat, BiocStyle, knitr, rmarkdown License: file LICENSE MD5sum: 87792c8bd9d78c5b5ffdf069ce52fa8d NeedsCompilation: no Package: alevinQC Version: 1.0.0 Depends: R (>= 3.6) Imports: rmarkdown, tools, methods, ggplot2, GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.11.5), cowplot Suggests: knitr, BiocStyle, testthat, License: MIT + file LICENSE MD5sum: 89abd6266744805e6da89f345a75b12c NeedsCompilation: no Package: AllelicImbalance Version: 1.22.0 Depends: R (>= 3.2.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 807f1eb3d123bed77822e239fc05029b NeedsCompilation: no Package: alpine Version: 1.10.0 Depends: R (>= 3.3) Imports: Biostrings, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm, splines, graph, RBGL, stringr, stats, methods, graphics, GenomeInfoDb, S4Vectors Suggests: knitr, testthat, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer License: GPL (>= 2) MD5sum: 406b4cea9ae12ceead4a586e194c567d NeedsCompilation: no Package: alsace Version: 1.20.0 Depends: R (>= 2.10), ALS, ptw (>= 1.0.6) Suggests: lattice, knitr License: GPL (>= 2) MD5sum: d93cfabbc11b8b2d27bfabde5067437c NeedsCompilation: no Package: altcdfenvs Version: 2.46.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: 47a0200f44c54dd06492e69bd03cd051 NeedsCompilation: no Package: AMARETTO Version: 1.0.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr License: Apache License (== 2.0) + file LICENSE MD5sum: 58c63ba233527e4f2b24d85aad2d857c NeedsCompilation: no Package: AMOUNTAIN Version: 1.10.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: 4511063e0919b9b89aacee901f2273b3 NeedsCompilation: yes Package: amplican Version: 1.6.2 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: cdd1b6aa2e182879ce87c016fca65307 NeedsCompilation: yes Package: AnalysisPageServer Version: 1.18.1 Imports: methods, log4r, tools, rjson, Biobase, graph Suggests: RUnit, XML, knitr Enhances: Rook (>= 1.1), fork, FastRWeb, ggplot2 License: Artistic-2.0 MD5sum: 1adba7952cc6d3d0dd3cbe33eaff5c3d NeedsCompilation: yes Package: anamiR Version: 1.12.0 Depends: R (>= 3.5) Imports: stats, DBI, limma, lumi, agricolae, RMySQL, DESeq2, SummarizedExperiment, gplots, gage, S4Vectors Suggests: knitr, rmarkdown, data.table License: GPL-2 MD5sum: 06285506bef8fafd7d42ee689fb9b63b NeedsCompilation: no Package: Anaquin Version: 2.8.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: a151bd5028a663f00df34bd73274a841 NeedsCompilation: no Package: AneuFinder Version: 1.12.1 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 0382a82d25493e6ecbfdbfe1781de546 NeedsCompilation: yes Package: ANF Version: 1.6.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8faf0a5e89310c253b504a30aa8e0287 NeedsCompilation: no Package: animalcules Version: 1.0.6 Depends: R (>= 3.6.0) Imports: assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2, rentrez, reshape2, covr, ape, vegan, dplyr, magrittr, MultiAssayExperiment, SummarizedExperiment, S4Vectors, XML, forcats, scales, lattice, glmnet, tsne, DMwR, plotROC, DT, utils, limma, methods, stats, tibble, httr Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 60c7d9b3d4691fc2ab67834d83122d64 NeedsCompilation: no Package: annaffy Version: 1.56.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: a8a02ef5f29978804a1d2c8e013829a5 NeedsCompilation: no Package: annmap Version: 1.26.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 721ffaaaab01aabd5bbbf20d7c25d1ce NeedsCompilation: no Package: annotate Version: 1.62.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 MD5sum: 8f03aad5fa522e027f0446f15eeaa1ea NeedsCompilation: no Package: AnnotationDbi Version: 1.46.1 Depends: R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25) Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7ef311d298823f19709ff4f45df75609 NeedsCompilation: no Package: AnnotationFilter Version: 1.8.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db License: Artistic-2.0 MD5sum: 603cfc35bf42d7549f2643e31b79a7a3 NeedsCompilation: no Package: AnnotationForge Version: 1.26.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager License: Artistic-2.0 MD5sum: f2394220b4915aa9338cf5173a83dcd5 NeedsCompilation: no Package: AnnotationFuncs Version: 1.34.0 Depends: R (>= 2.7.0), AnnotationDbi Imports: DBI Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 MD5sum: be945cfe20ec22abb94c68865e053fac NeedsCompilation: no Package: AnnotationHub Version: 2.16.1 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: d5acec73d9bdb0307a8f656c1dde34c0 NeedsCompilation: yes Package: AnnotationHubData Version: 1.14.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData License: Artistic-2.0 MD5sum: 8b2804206858012619e1ea021ac13d3f NeedsCompilation: no Package: annotationTools Version: 1.58.0 Imports: Biobase, stats License: GPL MD5sum: a3d93246437cc2a1e60e4c83e1dc14c2 NeedsCompilation: no Package: annotatr Version: 1.10.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.17.5), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: bebb93f6f3a99c3cdb56158c49e26029 NeedsCompilation: no Package: anota Version: 1.32.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 6b3a90ec4a197d10eb21ba9197e542c2 NeedsCompilation: no Package: anota2seq Version: 1.6.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: 10fc0941a5f771a929f463e9a386b763 NeedsCompilation: no Package: antiProfiles Version: 1.24.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: bdd8104b20e733ee81f7ebfd42810921 NeedsCompilation: no Package: apComplex Version: 2.50.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 97c9a7b9d83a2e280c6731ba19fd40a6 NeedsCompilation: no Package: apeglm Version: 1.6.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: be62827e5f20cdd38a44f3c163417486 NeedsCompilation: yes Package: appreci8R Version: 1.2.2 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db License: LGPL-3 MD5sum: 57e7f1c7522457aa3806c99d3aab30c6 NeedsCompilation: no Package: aroma.light Version: 3.14.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.22.0), R.utils (>= 2.7.0), matrixStats (>= 0.54.0) Suggests: princurve (>= 2.1.2) License: GPL (>= 2) MD5sum: b088ab52f1b5adc3ec73956627927728 NeedsCompilation: no Package: ArrayExpress Version: 1.44.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, oligo, limma Suggests: affy License: Artistic-2.0 MD5sum: 76ff83867cd18b53bffdab25bd564245 NeedsCompilation: no Package: ArrayExpressHTS Version: 1.34.2 Depends: sampling, Rsamtools (>= 1.99.0), snow Imports: Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops LinkingTo: Rhtslib (>= 1.15.3) License: Artistic License 2.0 MD5sum: 21ecd501928c5b7eb99ab88236041f1b NeedsCompilation: yes Package: arrayMvout Version: 1.42.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 27e2ed35f77af3c61d937e7694dfd814 NeedsCompilation: no Package: arrayQuality Version: 1.62.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 23f5d66736b23ca32f6db3b55b2f0b59 NeedsCompilation: no Package: arrayQualityMetrics Version: 3.40.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: feb4513176dad1e95c490dcf866092cc NeedsCompilation: no Package: ArrayTools Version: 1.44.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) MD5sum: 3e41b9280d67c39c0002721d521906d5 NeedsCompilation: no Package: ArrayTV Version: 1.22.0 Depends: R (>= 2.14) Imports: methods, foreach, S4Vectors (>= 0.9.25), IRanges (>= 2.13.24), DNAcopy, oligoClasses (>= 1.21.3) Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics Enhances: doMC, doSNOW, doParallel License: GPL (>= 2) MD5sum: e73af58a14b0d432bb15491156f492bc NeedsCompilation: no Package: ARRmNormalization Version: 1.24.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: fa44aea8216cb0a17a0719b10e276e89 NeedsCompilation: no Package: artMS Version: 1.2.7 Depends: R (>= 3.6.0) Imports: AnnotationDbi, biomaRt, bit64, circlize, cluster, ComplexHeatmap, corrplot, data.table, dplyr, factoextra, FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel, gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 63c7b44314ec08963fe700eef1a6065c NeedsCompilation: no Package: ASAFE Version: 1.10.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 607a5a93f3de7de64f09dea96c0526d6 NeedsCompilation: no Package: ASEB Version: 1.28.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 72879a9c7bf18ea45b4cd0fd9855fe3c NeedsCompilation: yes Package: ASGSCA Version: 1.18.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 8684a6a76f7d751d64bd09bf5f090a7e NeedsCompilation: no Package: ASICS Version: 2.0.1 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, grDevices, gridExtra, methods, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, TSdist, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: 71eb78f4f9359b06cde805d19d9e5d8f NeedsCompilation: no Package: ASpli Version: 1.10.0 Depends: methods, grDevices, stats, utils, parallel, edgeR Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools, BiocStyle License: GPL MD5sum: 552cdc96a5dfd1b28a87c9f9928e3036 NeedsCompilation: no Package: AssessORF Version: 1.2.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 7fe2617641b7963168599745ebbc2598 NeedsCompilation: no Package: ASSET Version: 2.2.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 962772db656337d51d15eac8b0a3fc86 NeedsCompilation: no Package: ASSIGN Version: 1.20.1 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 92fc35d4e6b9944a41e5cf84e702f25a NeedsCompilation: no Package: ATACseqQC Version: 1.8.5 Depends: R (>= 3.4), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat License: GPL (>= 2) MD5sum: 3438da92fc2782eef32ec360e2461817 NeedsCompilation: no Package: atSNP Version: 1.0.0 Depends: R (>= 3.6) Imports: Rcpp, data.table, BiocParallel, BiocFileCache, rappdirs, BSgenome, motifStack, grDevices, graphics, stats, utils, grid LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 3af26fbd4c4878de74d0e4abedef8462 NeedsCompilation: yes Package: attract Version: 1.36.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 84ae2e3cffca1dc87cc4adc53a2da5ee NeedsCompilation: no Package: AUCell Version: 1.6.1 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, utils Suggests: Biobase, BiocStyle, devtools, dynamicTreeCut, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 1b362074c0d854fdc60789f81a924b05 NeedsCompilation: no Package: BaalChIP Version: 1.10.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d9cae5f88c75467961335bd0e1bd88de NeedsCompilation: no Package: BAC Version: 1.44.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 7503cab362d622450435212c7aca4436 NeedsCompilation: yes Package: bacon Version: 1.12.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 86a2cea86bb1adf7f064f2558665b7c0 NeedsCompilation: yes Package: BADER Version: 1.22.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: c12c151e27efae47af5137305a7d6f75 NeedsCompilation: yes Package: BadRegionFinder Version: 1.12.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 6e3813a39cffe2ded4ee72248cf704e2 NeedsCompilation: no Package: BAGS Version: 2.24.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: bf7b643c639d196d99411a851f5215cb NeedsCompilation: yes Package: ballgown Version: 2.16.0 Depends: R (>= 3.1.1), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr License: Artistic-2.0 MD5sum: 80c05edb3007ae4bd8774ee870d4c9de NeedsCompilation: no Package: bamsignals Version: 1.16.0 Depends: R (>= 3.2.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: d193458eb5ac2b8af0c95ed0a6ef48dd NeedsCompilation: yes Package: BANDITS Version: 1.0.0 Depends: R (>= 3.6.0) Imports: Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: d2a9930abcadaa225c59afe1fd0e6097 NeedsCompilation: yes Package: banocc Version: 1.8.1 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat License: MIT + file LICENSE MD5sum: d4c66dbf5a039ebe40d7422dd1b394f5 NeedsCompilation: no Package: basecallQC Version: 1.8.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 1833033cf86b2c75d24b284a3bb3700f NeedsCompilation: no Package: BaseSpaceR Version: 1.28.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: bf914f2845df6896b289430c7dda8fb7 NeedsCompilation: no Package: Basic4Cseq Version: 1.20.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 60ecce3e0bfa529c4a4a99c72a55b046 NeedsCompilation: no Package: BASiCS Version: 1.6.0 Depends: R (>= 3.6), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, data.table, ggExtra, ggplot2, graphics, grDevices, KernSmooth, MASS, matrixStats, methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4, SummarizedExperiment, viridis, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 2313c99d85e93025a11ad67d50a931ad NeedsCompilation: yes Package: BasicSTARRseq Version: 1.12.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: d2511adf3fc8177f9135ba710a978b98 NeedsCompilation: no Package: batchelor Version: 1.0.1 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, scater, BiocParallel LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, beachmat, scRNAseq License: GPL-3 MD5sum: 60f36d9c6ef3150cf85106a496deb95f NeedsCompilation: yes Package: BatchQC Version: 1.12.1 Depends: R (>= 3.3.0) Imports: utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva, corpcor, moments, matrixStats, ggvis, d3heatmap, reshape2, limma, grDevices, graphics, stats, methods, Matrix Suggests: testthat License: GPL (>= 2) MD5sum: d431a82b8202cab61a08360e0037ec3b NeedsCompilation: no Package: BayesKnockdown Version: 1.10.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: c3790c39334419427105d2404a4e8155 NeedsCompilation: no Package: BayesPeak Version: 1.36.0 Depends: R (>= 2.14), IRanges Imports: IRanges, graphics Suggests: BiocStyle, parallel License: GPL (>= 2) MD5sum: 5cbdcb27c5f5fd239bb1a3b0521d5e3c NeedsCompilation: yes Package: bayNorm Version: 1.2.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 32d5215e13ae5eccf197f760b8c2f368 NeedsCompilation: yes Package: baySeq Version: 2.18.0 Depends: R (>= 2.3.0), methods, GenomicRanges, abind, parallel Imports: edgeR Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: db957567c040f3240610ab767f1bb0c4 NeedsCompilation: no Package: BBCAnalyzer Version: 1.14.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 350d7307122713cb15aab5eee510c524 NeedsCompilation: no Package: BCRANK Version: 1.46.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 1e9103225b4ac26e8252a559d9622498 NeedsCompilation: yes Package: bcSeq Version: 1.6.0 Depends: R (>= 3.4.2) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 522909473d50d079a1b737a997d24414 NeedsCompilation: yes Package: BDMMAcorrect Version: 1.2.0 Depends: R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment Imports: Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats LinkingTo: Rcpp, RcppArmadillo, RcppEigen Suggests: knitr, rmarkdown, BiocGenerics License: GPL (>= 2) MD5sum: 08b2cfecf96d63befb59e857ad9b7bf4 NeedsCompilation: yes Package: beachmat Version: 2.0.0 Imports: methods, DelayedArray, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools License: GPL-3 MD5sum: c0c0ea857cbfc243f4350ef48527b6f5 NeedsCompilation: yes Package: beadarray Version: 2.34.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 4f03d3bd7e45479f800e943ef7e4384d NeedsCompilation: yes Package: beadarraySNP Version: 1.50.0 Depends: methods, Biobase (>= 2.14), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 MD5sum: be8d5f6c4373eb5b19bef26fe6f9fb48 NeedsCompilation: no Package: BeadDataPackR Version: 1.36.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: caf869b373fa5fbd3820f7760d2cf84f NeedsCompilation: yes Package: BEARscc Version: 1.4.0 Imports: ggplot2, SingleCellExperiment, data.table, stats, utils, graphics, compiler Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF License: GPL-3 MD5sum: 74b837640990a0c334f1ec70bc269165 NeedsCompilation: no Package: BEAT Version: 1.22.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 5ca0f1e34e04fd2c3293960760fd7b80 NeedsCompilation: no Package: BEclear Version: 2.0.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, stats, graphics, utils, methods LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander License: GPL-3 MD5sum: 92515d8f34e66403c62df8b192d0dbdf NeedsCompilation: yes Package: bgafun Version: 1.46.0 Depends: made4, seqinr,ade4 License: Artistic-2.0 MD5sum: 62e6be628d01e80d2193cd34d29602ac NeedsCompilation: no Package: BgeeDB Version: 2.10.0 Depends: R (>= 3.3.0), topGO, tidyr Imports: data.table, RCurl, digest, methods, stats, utils, dplyr, graph, Biobase Suggests: knitr, BiocStyle, testthat, rmarkdown License: GPL-3 MD5sum: 4da20080e790bd0121458d873a9d525b NeedsCompilation: no Package: BGmix Version: 1.44.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 MD5sum: ed5d6b4d0fdcbc4b26fa57154d9e8cba NeedsCompilation: yes Package: bgx Version: 1.50.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: 0249dde7f7644bf8aee843004a9deb93 NeedsCompilation: yes Package: BHC Version: 1.36.0 License: GPL-3 MD5sum: 068199f15d449715b3a74a4065f548ec NeedsCompilation: yes Package: BicARE Version: 1.42.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 MD5sum: db034e853c41bbe8c9bbd029b4810082 NeedsCompilation: yes Package: BiFET Version: 1.4.0 Imports: stats, poibin, GenomicRanges Suggests: testthat, knitr License: GPL-3 MD5sum: 9d5de94f76d910215de96b965bc1eaab NeedsCompilation: no Package: BiGGR Version: 1.20.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr Imports: hypergraph, limSolve License: file LICENSE MD5sum: b10464c305eafcdb9f52d932a36f0382 NeedsCompilation: no Package: bigmelon Version: 1.10.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics Suggests: BiocGenerics, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: fb80cb687a5702ad151f2217b577da3e NeedsCompilation: no Package: bigmemoryExtras Version: 1.32.0 Depends: R (>= 2.12), bigmemory (>= 4.5.31) Imports: methods Suggests: testthat, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 OS_type: unix MD5sum: f8f4f43d3318d5118883e89803205d49 NeedsCompilation: no Package: bigPint Version: 1.0.0 Depends: R (>= 3.5.2) Imports: dplyr (>= 0.7.2), GGally (>= 1.3.2), ggplot2 (>= 2.2.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), grid (>= 3.5.0), gridExtra (>= 2.3), hexbin (>= 1.27.1), Hmisc (>= 4.0.3), htmlwidgets (>= 0.9), methods (>= 3.5.2), plotly (>= 4.7.1), plyr (>= 1.8.4), RColorBrewer (>= 1.1.2), reshape (>= 0.8.7), shiny (>= 1.0.5), shinycssloaders (>= 0.2.0), shinydashboard (>= 0.6.1), stats (>= 3.5.0), stringr (>= 1.3.1), tidyr (>= 0.7.0), utils (>= 3.5.0) Suggests: BiocGenerics (>= 0.29.1), data.table (>= 1.11.8), EDASeq (>= 2.14.0), edgeR (>= 3.22.2), gtools (>= 3.5.0), knitr (>= 1.13), matrixStats (>= 0.53.1), rmarkdown (>= 1.10), roxygen2 (>= 3.0.0), RUnit (>= 0.4.32), tibble (>= 1.4.2), License: GPL-3 MD5sum: e088f5debc65a3f6b74f6f47b9949bc3 NeedsCompilation: no Package: bioassayR Version: 1.22.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown License: Artistic-2.0 MD5sum: 78c3d0f8997a2ad15ca8cce89222bc9c NeedsCompilation: no Package: Biobase Version: 2.44.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets License: Artistic-2.0 MD5sum: 2f8f240f9146ececcd4e297c86705ae0 NeedsCompilation: yes Package: biobroom Version: 1.16.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, SummarizedExperiment License: LGPL MD5sum: 4541701fe3cbd912a008c0254029b54a NeedsCompilation: no Package: bioCancer Version: 1.12.0 Depends: R (>= 3.4.0), radiant.data (>= 0.9.1), cgdsr(>= 1.2.6), XML(>= 3.98) Imports: DT (>= 0.3), dplyr (>= 0.7.2), shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, shinythemes, Biobase, geNetClassifier, AnnotationFuncs, org.Hs.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(>= 0.7), visNetwork, htmlwidgets, plyr, tibble Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: ff8c79305222e25cf02716f9ceb953e6 NeedsCompilation: no Package: BiocCaseStudies Version: 1.46.0 Depends: tools, methods, utils, Biobase Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) License: Artistic-2.0 MD5sum: 04e12153b18240289d6891b6000e5e1a NeedsCompilation: no Package: BiocCheck Version: 1.20.0 Depends: R (>= 3.5.0) Imports: biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr, tools, optparse, codetools, methods, utils, knitr Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1), usethis, BiocStyle Enhances: codetoolsBioC License: Artistic-2.0 MD5sum: f7f9dcecc38c06d20364dc756d21f324 NeedsCompilation: no Package: BiocFileCache Version: 1.8.0 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: e362534e2cd232efbe27190cbd15fbb9 NeedsCompilation: no Package: BiocGenerics Version: 0.30.0 Depends: R (>= 3.6.0), methods, utils, graphics, stats, parallel Imports: methods, utils, graphics, stats, parallel Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit License: Artistic-2.0 MD5sum: 77e2d121cec79b2656c24621b77923da NeedsCompilation: no Package: biocGraph Version: 1.46.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: 8c4c19f08f543393ec056e3c14fcafca NeedsCompilation: no Package: BiocNeighbors Version: 1.2.0 Imports: Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods LinkingTo: Rcpp, RcppAnnoy, RcppHNSW Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW License: GPL-3 MD5sum: ea04a1707a7374e2de38e2f0310eaf80 NeedsCompilation: yes Package: BiocOncoTK Version: 1.4.0 Depends: R (>= 3.5.0), methods Imports: ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures Suggests: knitr, dbplyr, DBI, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75 License: Artistic-2.0 MD5sum: 16fba5eb15058c62c7f28924a3c28223 NeedsCompilation: no Package: BioCor Version: 1.8.1 Depends: R (>= 3.4.0) Imports: BiocParallel, Matrix, GSEABase Suggests: reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling License: MIT + file LICENSE MD5sum: 379330238ba3a7de619f7259087eb598 NeedsCompilation: no Package: BiocParallel Version: 1.18.1 Depends: methods Imports: stats, utils, futile.logger, parallel, snow LinkingTo: BH Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table License: GPL-2 | GPL-3 MD5sum: 5bf35a35d23a4df933e944a4b3cc6e28 NeedsCompilation: yes Package: BiocPkgTools Version: 1.2.0 Depends: htmlwidgets Imports: BiocManager, biocViews, tibble, stringr, rvest, rex, dplyr, xml2, readr, httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh, RBGL, graph, magrittr Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC, pdftools, visNetwork, clipr License: MIT + file LICENSE MD5sum: 579be6f301bf4c99ebdfd01c757b751c NeedsCompilation: no Package: BiocSingular Version: 1.0.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, beachmat License: GPL-3 MD5sum: 529a83b1188e9db77f65c5b51fa67ded NeedsCompilation: yes Package: BiocSklearn Version: 1.6.0 Depends: R (>= 3.5.0), reticulate, methods, SummarizedExperiment, knitr Imports: BBmisc Suggests: testthat, restfulSE, HDF5Array, BiocStyle License: Artistic-2.0 MD5sum: 08d1933cf9d02f67c3eb8bbda351afd5 NeedsCompilation: no Package: BiocStyle Version: 2.12.0 Imports: bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 MD5sum: ef988ecd950940e6d7f9dcaa76bbdeb4 NeedsCompilation: no Package: BiocVersion Version: 3.9.0 Depends: R (>= 3.6.0), R (< 3.7.0) License: Artistic-2.0 MD5sum: 82c8be204ec54af118c304eee89b1ca7 NeedsCompilation: no Package: biocViews Version: 1.52.2 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark License: Artistic-2.0 MD5sum: 620818e4fd029a3acf46d437c08752a7 NeedsCompilation: no Package: BiocWorkflowTools Version: 1.10.0 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, devtools, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE MD5sum: b35b8354e016215f29f0fa4c7108e4ef NeedsCompilation: no Package: bioDist Version: 1.56.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: 2d840412a1cb4aa5a70a225fa5be7a4b NeedsCompilation: no Package: biomaRt Version: 2.40.5 Depends: methods Imports: utils, XML, RCurl, AnnotationDbi, progress, stringr, httr Suggests: annotate, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 61a1672e25543a3bf29655c784ab43a0 NeedsCompilation: no Package: biomformat Version: 1.12.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: d2a93f141e43ac49d4e7ded308ecb29f NeedsCompilation: no Package: BioMM Version: 1.0.0 Depends: R (>= 3.6) Imports: stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, nsprcomp, ranger, e1071, variancePartition, ggplot2 Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: c82d385b2460620296de121163c9b500 NeedsCompilation: no Package: BioMVCClass Version: 1.52.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: dc40cf1df6b1793993401d3f8438625f NeedsCompilation: no Package: biomvRCNS Version: 1.24.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: abf2ba8352f9473e8e489f55569a307e NeedsCompilation: yes Package: BioNet Version: 1.44.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 33b3f5065ff53b5414ca11432a489261 NeedsCompilation: no Package: BioNetStat Version: 1.4.3 Depends: R (>= 3.5), shiny, igraph, shinyBS, pathview Imports: BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr, utils, stats, RColorBrewer, Hmisc, psych, knitr License: GPL (>= 3) MD5sum: ef62a7abf394d7b0a9908309744596c2 NeedsCompilation: no Package: BioQC Version: 1.12.0 Depends: utils, Rcpp, Biobase, methods, stats Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, hgu133plus2.db, ineq License: GPL (>= 3) MD5sum: acd4981f54d129a02e19563063f8be27 NeedsCompilation: yes Package: BioSeqClass Version: 1.42.0 Depends: R (>= 2.10), scatterplot3d Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices Suggests: scatterplot3d License: LGPL (>= 2.0) MD5sum: f84297e07369bf7aeeef25aad3e45261 NeedsCompilation: no Package: biosigner Version: 1.12.0 Depends: Biobase, ropls Imports: methods, e1071, randomForest Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, rmarkdown, testthat License: CeCILL MD5sum: 370b5493603495a810a607df9587e081 NeedsCompilation: no Package: Biostrings Version: 2.52.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13), IRanges, XVector (>= 0.23.2) Imports: graphics, methods, stats, utils LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: 288b4398c81188be1a32bfd27241492d NeedsCompilation: yes Package: biosvd Version: 2.20.0 Depends: R (>= 3.1.0) Imports: BiocGenerics, Biobase, methods, grid, graphics, NMF License: Artistic-2.0 MD5sum: c445ae7cb8f2f00107f38edc234a92c8 NeedsCompilation: no Package: biotmle Version: 1.8.0 Depends: R (>= 3.4) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma, tmle Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: file LICENSE MD5sum: c19bed4db37f90de3029d5374f65d94a NeedsCompilation: no Package: biovizBase Version: 1.32.0 Depends: R (>= 2.10), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: cae76703fef55cb32ba79461f815b86e NeedsCompilation: yes Package: BiRewire Version: 3.16.0 Depends: igraph, slam, tsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: f0ffa84bfc1b5a61653bfdc3fa10d25e NeedsCompilation: yes Package: birta Version: 1.28.0 Depends: limma, MASS, R(>= 2.10), Biobase, methods License: GPL (>= 2) MD5sum: d4c84a404a92d5698e1af22fd17da36b NeedsCompilation: yes Package: BiSeq Version: 1.24.0 Depends: R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: c460a1ce9835304b0c0caaed08b7e828 NeedsCompilation: no Package: BitSeq Version: 1.28.0 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle License: Artistic-2.0 + file LICENSE MD5sum: 813708121ae472700424da3cde5fdf22 NeedsCompilation: yes Package: blima Version: 1.18.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: 2e95ea07342f80f96e6893c08a11ef12 NeedsCompilation: yes Package: BLMA Version: 1.8.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 03448e027232a4ce824f5981f73f3858 NeedsCompilation: no Package: bnbc Version: 1.6.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 2ac97c91b275868cae06795309f84f1c NeedsCompilation: yes Package: BPRMeth Version: 1.10.0 Depends: R (>= 3.4.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: bbcac2501e39ec8cc0610666f24dafa7 NeedsCompilation: yes Package: BRAIN Version: 1.30.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 66a32ce11265c7b523f7e4736aa777c4 NeedsCompilation: no Package: brainImageR Version: 1.1.0 Depends: R (>= 3.5) Imports: BiocGenerics, ExperimentHub, ggplot2, grDevices, grid, gridExtra, methods, randomForest, RColorBrewer, stats, testthat Suggests: knitr, rmarkdown License: CC BY-SA 4.0 MD5sum: 4e4558bdb154e1bad002543fca8f1c10 NeedsCompilation: no Package: BrainStars Version: 1.28.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 MD5sum: 56f8fb333636c6039354361fb6ea6c7e NeedsCompilation: no Package: branchpointer Version: 1.10.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 3b81c925b5c40c1767e6b923782bf57e NeedsCompilation: no Package: breakpointR Version: 1.2.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: acb110bb2c43c9bfac81309de7281960 NeedsCompilation: no Package: bridge Version: 1.48.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: 480a9c00864b54d93b8c319a3db68795 NeedsCompilation: yes Package: BridgeDbR Version: 1.18.0 Depends: R (>= 3.3.0), rJava Imports: RCurl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 791900b33b1997d6e5308c888d4ca2ea NeedsCompilation: no Package: BrowserViz Version: 2.6.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle License: GPL-2 MD5sum: 263756ed6328875b0b8f1890a17f3ef5 NeedsCompilation: no Package: BSgenome Version: 1.52.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit License: Artistic-2.0 MD5sum: 6af1de03fa89f6a029a86d70ea8e9fe8 NeedsCompilation: no Package: bsseq Version: 1.20.0 Depends: R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.29.14), SummarizedExperiment (>= 1.9.18) Imports: IRanges (>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors, R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.9.8), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.11.9), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs License: Artistic-2.0 MD5sum: fafc60de775b2523fd161a7711106a9a NeedsCompilation: yes Package: BubbleTree Version: 2.14.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.7.5), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 742ca18c07acb22717ae1dea849bed4a NeedsCompilation: no Package: BufferedMatrix Version: 1.48.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: c4fbf25d9fb604528e65ad5c8fb14309 NeedsCompilation: yes Package: BufferedMatrixMethods Version: 1.48.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 8a3abe17de06403a2ea5ead96663ef3f NeedsCompilation: yes Package: BUMHMM Version: 1.8.0 Depends: R (>= 3.4) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: abc7caecb419e680be1f0a5523c2a71a NeedsCompilation: no Package: bumphunter Version: 1.26.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: e25e9e6a64a16dcef24c87e798527c93 NeedsCompilation: no Package: BUS Version: 1.40.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: ff29430aa926268c7089a76acc9f2844 NeedsCompilation: yes Package: BUScorrect Version: 1.2.1 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: acc675473fb5e47ec6e364c4edbe4461 NeedsCompilation: yes Package: CAFE Version: 1.20.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 4aa05a6bf30967eec73b6a616e1c0a00 NeedsCompilation: no Package: CAGEfightR Version: 1.4.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods, Matrix(>= 1.2-12), Matrix.utils(>= 0.9.6), grr(>= 0.9.5), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: b4d4fe760ca5f2d924c4ad980502a530 NeedsCompilation: no Package: CAGEr Version: 1.26.0 Depends: methods, R (>= 2.15.0) Imports: beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.23.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.5.27), KernSmooth, memoise, MultiAssayExperiment, plyr, Rsamtools, reshape, rtracklayer, S4Vectors, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: a772349f5b6bdf941e81f52030ee226a NeedsCompilation: no Package: CALIB Version: 1.50.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL MD5sum: 9c5e453a09daa9f258cc2c396d127781 NeedsCompilation: yes Package: CAMERA Version: 1.40.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: b69c86dafe1b112ee23bfce67a9725a3 NeedsCompilation: yes Package: CAMTHC Version: 1.2.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 29259f9a6a2be58c0e648edf17b0adc9 NeedsCompilation: no Package: canceR Version: 1.18.6 Depends: R (>= 3.4), tcltk, tcltk2, cgdsr Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, graphics, stats, utils, grDevices Suggests: testthat (>= 0.10.0), R.rsp License: GPL-2 MD5sum: 224f80420e3ed97661de974c54b61d6d NeedsCompilation: no Package: cancerclass Version: 1.28.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 96e541e72420dee85bc2abcb91ff3f36 NeedsCompilation: yes Package: CancerInSilico Version: 2.4.0 Depends: R (>= 3.4), Rcpp Imports: methods, utils, graphics, stats LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl License: GPL-2 MD5sum: 19bdc49294e17f67b6cffbc0fd53e67b NeedsCompilation: yes Package: CancerMutationAnalysis Version: 1.26.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE MD5sum: b68cb94aaffc396c1fb4db092acbae91 NeedsCompilation: yes Package: CancerSubtypes Version: 1.10.0 Depends: R (>= 3.4), sigclust, NMF Imports: SNFtool, iCluster, cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical License: GPL (>= 2) MD5sum: cfa0a35941d1046859161ffd2fbacb9f NeedsCompilation: no Package: CAnD Version: 1.16.0 Imports: methods, ggplot2, reshape Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 MD5sum: b37b73d94fb166e98936f40b91f3f3f3 NeedsCompilation: no Package: caOmicsV Version: 1.14.0 Depends: R (>= 3.2), igraph (>= 0.7.1), bc3net (>= 1.0.2) License: GPL (>= 2.0) MD5sum: 94c63ecbfe0401c88974fa774831ed1e NeedsCompilation: no Package: Cardinal Version: 2.2.6 Depends: BiocGenerics, BiocParallel, EBImage, graphics, methods, S4Vectors, stats, ProtGenerics Imports: Biobase, dplyr, grid, irlba, lattice, Matrix, matter, magrittr, mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: f4dd2c9ae659f7fdb6df6075bb89ccd1 NeedsCompilation: yes Package: casper Version: 2.18.0 Depends: R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics, coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: 6217e8fdb4348566354428667313e3f4 NeedsCompilation: yes Package: CATALYST Version: 1.8.7 Depends: R (>= 3.6) Imports: Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus, data.table, dplyr, drc, DT, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, htmltools, limma, magrittr, matrixStats, methods, nnls, plotly, purrr, RColorBrewer, reshape2, Rtsne, S4Vectors, scales, scater, shiny, shinydashboard, shinyBS, shinyjs, SingleCellExperiment, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt, umap License: GPL (>= 2) MD5sum: 48da7eb743226e02a705ce5aef82422a NeedsCompilation: no Package: Category Version: 2.50.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 610c7927a696661781795a3d1ca41539 NeedsCompilation: no Package: categoryCompare Version: 1.28.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 MD5sum: d3bd6209e65811fef8df62ffb93bd150 NeedsCompilation: no Package: CausalR Version: 1.16.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e1eee612fc9cb8f492e5d61d5cb07823 NeedsCompilation: no Package: cbaf Version: 1.6.0 Imports: BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots, grDevices, stats, utils, xlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 41ce506cab60b7ac4d85c024f43eca84 NeedsCompilation: no Package: ccfindR Version: 1.4.2 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 5c96d645ad4077e82910b32f4f7ae838 NeedsCompilation: yes Package: ccmap Version: 1.10.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.24.0), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: 4d904def7978b58e57ea2bd1a941179f NeedsCompilation: no Package: CCPROMISE Version: 1.10.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: c914d856d7feb2613b26d682f881a9ee NeedsCompilation: no Package: ccrepe Version: 1.20.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE MD5sum: a6aec5acadb248eb94a14fa114bbc658 NeedsCompilation: no Package: celaref Version: 1.2.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 050a0789e0fa54d29ff8ddb134e05710 NeedsCompilation: no Package: celda Version: 1.0.4 Depends: R (>= 3.6) Imports: stats, plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, gridExtra, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, umap, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle License: MIT + file LICENSE MD5sum: 678f559bbbd77209da6b871e4be4b328 NeedsCompilation: yes Package: cellbaseR Version: 1.8.1 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: dffc1e9b4f0af7c68c108d442d4f4e12 NeedsCompilation: no Package: CellBench Version: 1.0.1 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: ce224530fd6d16b0080f167744bf8d8e NeedsCompilation: no Package: cellGrowth Version: 1.28.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 MD5sum: 25a0f256421f38c8a6fd36b95900aacc NeedsCompilation: no Package: cellHTS2 Version: 2.48.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2 License: Artistic-2.0 MD5sum: 47d1c36b22194c71761ee17bf05f35b0 NeedsCompilation: no Package: cellity Version: 1.12.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 292c57c85e717761e9acefbfab0e4894 NeedsCompilation: no Package: CellMapper Version: 1.10.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 46b337915bc344f73f8942e2f20f7f09 NeedsCompilation: no Package: CellMixS Version: 1.0.2 Depends: kSamples, R (>= 3.6) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, listarrays, methods, BiocParallel Suggests: BiocStyle, knitr, rmarkdown, testthat, limma License: GPL (>= 2) MD5sum: 5fb75dda1afd0d8a2179312ea797428a NeedsCompilation: no Package: CellNOptR Version: 1.30.0 Depends: R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2 Imports: igraph, stringi, stringr, Suggests: data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics, License: GPL-3 MD5sum: 9b0dba0616690fed7ae50cc60e5def8a NeedsCompilation: yes Package: cellscape Version: 1.8.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0), plyr (>= 1.8.3), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a3879c530dadeea94b728acea78ef4cc NeedsCompilation: no Package: CellScore Version: 1.4.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0) Suggests: hgu133plus2CellScore, knitr License: GPL-3 MD5sum: a574b7a8e836c7ab3c26c00a14810ac0 NeedsCompilation: no Package: CellTrails Version: 1.2.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: e64c7c273fb506b9cc1931e4ec63558d NeedsCompilation: no Package: cellTree Version: 1.14.0 Depends: R (>= 3.3), topGO Imports: topicmodels, slam, maptpx, igraph, xtable, gplots Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools License: Artistic-2.0 MD5sum: 0d509562248089909780d86511d479f6 NeedsCompilation: no Package: CEMiTool Version: 1.8.3 Depends: R (>= 3.5) Imports: methods, scales, gRbase, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, GeneOverlap, limma, tidyr, plyr, ff, ffbase, RColorBrewer Suggests: testthat, BiocManager License: GPL-3 MD5sum: f14733b388f546a0f5c343003a5db8cc NeedsCompilation: no Package: CexoR Version: 1.22.0 Depends: R (>= 2.10.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: d511dfadd09f06ab9ab73f2de560b815 NeedsCompilation: no Package: CFAssay Version: 1.18.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: c0704e737f2e2b56f14e679d98a7b092 NeedsCompilation: no Package: CGEN Version: 3.20.0 Depends: R (>= 2.10.1), survival, mvtnorm Suggests: cluster License: GPL-2 + file LICENSE MD5sum: 767b43ecdbf0996bfd4cca6de398c669 NeedsCompilation: yes Package: CGHbase Version: 1.44.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 6407dc3137d1d4cdbea47d20cb2a2a81 NeedsCompilation: no Package: CGHcall Version: 2.46.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: 892aae691ef9ebd057fa867b487e309e NeedsCompilation: no Package: cghMCR Version: 1.42.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: eaf9fbdce3b0f3a370e021769e05db83 NeedsCompilation: no Package: CGHnormaliter Version: 1.38.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: ced0a49c575405ab70d0728b3b32a9f9 NeedsCompilation: no Package: CGHregions Version: 1.42.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 78e9736273b569e7f6eba6f2024f2a40 NeedsCompilation: no Package: ChAMP Version: 2.14.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0), FEM (>= 3.1),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19, limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: c9aee84f402874745f1c5289f6de38b3 NeedsCompilation: no Package: CHARGE Version: 1.4.0 Depends: R (>= 3.5), GenomicRanges, methods Imports: SummarizedExperiment, FactoMineR, factoextra, IRanges, graphics, modes, parallel, plyr, cluster, diptest, stats, matrixStats Suggests: roxygen2, EnsDb.Hsapiens.v86 License: GPL-2 MD5sum: 68a0b860a2dc6ecc2e64eb5496954d0b NeedsCompilation: no Package: charm Version: 2.29.0 Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor License: LGPL (>= 2) MD5sum: f8013190e4d25c45eb4999a6a2c4a883 NeedsCompilation: no Package: ChemmineOB Version: 1.22.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp Suggests: ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap, BiocManager Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: 7fe4e4182986ff317665bf0db03aab31 NeedsCompilation: yes Package: ChemmineR Version: 3.36.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>= 1.16.1), ChemmineDrugs, png,rmarkdown, BiocManager Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 8d49bddc3a3375ead2711b55cd405930 NeedsCompilation: yes Package: CHETAH Version: 1.0.5 Depends: R (>= 3.6), ggplot2, SingleCellExperiment Imports: gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: fc30809f125280dd69c83b329291bb69 NeedsCompilation: no Package: ChIC Version: 1.4.0 Depends: spp, R (>= 3.5) Imports: ChIC.data (>= 1.3.3), caTools, methods,GenomicRanges, IRanges, parallel, progress, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics License: GPL-2 MD5sum: 36c70a76294c44a3740a1aca9aa5a9b5 NeedsCompilation: no Package: Chicago Version: 1.12.0 Depends: R (>= 3.2), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: d5ed2c8bd98b169b431f2aef87a65aa6 NeedsCompilation: no Package: chimera Version: 1.26.0 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens Suggests: BiocParallel, geneplotter Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 1260ef67ee085f1a61374ae3a7deafed NeedsCompilation: yes Package: chimeraviz Version: 1.10.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, ArgumentCheck, gtools Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 1232b731506b98afc592ea7cc9bb3732 NeedsCompilation: no Package: ChIPanalyser Version: 1.6.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 9bd347492da8d4964d74601513538ea7 NeedsCompilation: no Package: ChIPComp Version: 1.14.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 7cefdbab363e65223863f0845cb2c840 NeedsCompilation: yes Package: chipenrich Version: 2.8.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors, stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 70a5e2c7704314c3f01ab8571cc47769 NeedsCompilation: no Package: ChIPexoQual Version: 1.8.0 Depends: R (>= 3.4.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 9f41cb7adca04bb0dea5fd142061d18d NeedsCompilation: no Package: ChIPpeakAnno Version: 3.18.2 Depends: R (>= 3.2), methods, grid, IRanges (>= 2.13.12), Biostrings (>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25), VennDiagram Imports: BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocManager, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi License: GPL (>= 2) MD5sum: 463590183bc2d2eb623ea12549b292d2 NeedsCompilation: no Package: ChIPQC Version: 1.20.0 Depends: R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19) Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: 1eeef062ff28b32273a925872e9b4de0 NeedsCompilation: no Package: ChIPseeker Version: 1.20.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicFeatures (>= 1.31.3), ggplot2 (>= 2.2.0), gplots, graphics, grDevices, grid, gridBase, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors (>= 0.17.25), stats, TxDb.Hsapiens.UCSC.hg19.knownGene, UpSetR, utils Suggests: clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle, rmarkdown, testthat License: Artistic-2.0 MD5sum: bb0609bdaf4de9d9423bfd758bad1e12 NeedsCompilation: no Package: chipseq Version: 1.34.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 MD5sum: 0789cf5bd49a71364a763517cb219aea NeedsCompilation: yes Package: ChIPseqR Version: 1.38.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: b1ce207d55454fdc59df12255e6d3f0f NeedsCompilation: yes Package: ChIPSeqSpike Version: 1.4.0 Depends: R (>= 3.5), rtracklayer (>= 1.37.6) Imports: tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots, ggplot2, LSD, corrplot, methods, stats, grDevices, graphics, utils, BiocGenerics, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: f36d97df712bd1d40d5ccddda86dcc05 NeedsCompilation: no Package: ChIPsim Version: 1.38.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 21a19dd3b1a20aa6feabae9db8193bd3 NeedsCompilation: no Package: ChIPXpress Version: 1.28.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 9680fbb73971f9b76b2099d0b0ca8161 NeedsCompilation: no Package: chopsticks Version: 1.50.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 6971614767463f422261c871144d0de4 NeedsCompilation: yes Package: chroGPS Version: 2.2.0 Depends: R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS, graphics, stats, changepoint Imports: cluster, DPpackage, ICSNP, ellipse, vegan Enhances: parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno, org.Dm.eg.db, caTools, plotly License: GPL (>= 2.14) MD5sum: 1c20015597fc1f3d3e4f99320344c4bf NeedsCompilation: no Package: chromDraw Version: 2.14.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: e577a789a88f7d82e8e6fc7a9388cbb5 NeedsCompilation: yes Package: ChromHeatMap Version: 1.38.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: 86424fcf2665a84797efb9977b73449f NeedsCompilation: no Package: chromPlot Version: 1.12.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: a83b3a023294deec5184eb5f7af01ec1 NeedsCompilation: no Package: chromstaR Version: 1.10.0 Depends: R (>= 3.3), GenomicRanges, ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 MD5sum: 021eb8e6f24bb476a42ceefcaf19b883 NeedsCompilation: yes Package: chromswitch Version: 1.6.0 Depends: R (>= 3.4), GenomicRanges (>= 1.26.4) Imports: cluster (>= 2.0.6), Biobase (>= 2.36.2), BiocParallel (>= 1.8.2), dplyr (>= 0.5.0), gplots(>= 3.0.1), graphics, grDevices, IRanges (>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer (>= 1.36.4), S4Vectors (>= 0.14.4), stats, tidyr (>= 0.6.3) Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat License: MIT + file LICENSE MD5sum: a4818e3957bc869fe4f87d9c38066fc3 NeedsCompilation: no Package: chromVAR Version: 1.6.0 Depends: R (>= 3.4) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: 00a21c0ce9d872f74f6a5206daaaaaa4 NeedsCompilation: yes Package: CHRONOS Version: 1.12.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt Suggests: RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: 23549499ee1be61c2fe468de10d353b0 NeedsCompilation: no Package: cicero Version: 1.2.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringr (>= 1.2.0), tibble (>= 1.4.2), VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 20ceee0cf038811ec4b611da2d8248c7 NeedsCompilation: no Package: CINdex Version: 1.12.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens License: GPL (>= 2) MD5sum: 5194827a892d59246818e56c5c65cf59 NeedsCompilation: no Package: cisPath Version: 1.24.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: bf2dfa76883e6262aabd0a67e7e3e6be NeedsCompilation: yes Package: ClassifyR Version: 2.4.4 Depends: R (>= 3.6.0), methods, S4Vectors, MultiAssayExperiment, BiocParallel Imports: locfit, grid, utils, plyr Suggests: limma, genefilter, edgeR, car, Rmixmod, ggplot2, gridExtra, cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, glmnet, class License: GPL-3 MD5sum: 8a6e77df41678daff4030b332c3f9d1a NeedsCompilation: no Package: cleanUpdTSeq Version: 1.22.2 Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), methods, stats Imports: BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7 Suggests: BiocStyle, knitr, RUnit License: GPL-2 MD5sum: c33ff7362ec09fc2417d50a09df2e0e0 NeedsCompilation: no Package: cleaver Version: 1.22.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.1.4) License: GPL (>= 3) MD5sum: 9759e3cc9a1c9f2be7e029ceb462b4a3 NeedsCompilation: no Package: clippda Version: 1.34.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 9555259a3e4435bdbdd750f255b16918 NeedsCompilation: no Package: clipper Version: 1.24.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 5ffbf94bc0991428351e2c32de0cec5c NeedsCompilation: no Package: Clomial Version: 1.20.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 483932cc2911c5055e2972fbeb3005b2 NeedsCompilation: no Package: Clonality Version: 1.32.0 Depends: R (>= 2.12.2), DNAcopy Imports: grDevices, graphics, stats, utils Suggests: gdata License: GPL-3 MD5sum: 16951e83e9b7565b99dca3cb450eebf9 NeedsCompilation: no Package: clonotypeR Version: 1.22.0 Imports: methods Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan License: file LICENSE MD5sum: d123ef6f87bc8411f75011922537ad38 NeedsCompilation: no Package: clst Version: 1.32.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: a9b3a5b2342ff43e0946b8c17c81816c NeedsCompilation: no Package: clstutils Version: 1.32.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 MD5sum: f31a1566acdc40319644a1c7ec1969ab NeedsCompilation: no Package: CluMSID Version: 1.0.0 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE MD5sum: 48db07b1d9a97a89ad03a97253e8e24a NeedsCompilation: no Package: clustComp Version: 1.12.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5d6c72bdfdab1828b794fe80e5b2bf4e NeedsCompilation: no Package: clusterExperiment Version: 2.4.4 Depends: R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment, BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph License: Artistic-2.0 MD5sum: b9ca4e2ca15f286e586d636f3fb55ba2 NeedsCompilation: yes Package: ClusterJudge Version: 1.6.0 Depends: R (>= 3.4), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 8355965d9a38957058a66a8a28535160 NeedsCompilation: no Package: clusterProfiler Version: 3.12.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7), ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rvcheck, stats, tidyr, utils Suggests: AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat License: Artistic-2.0 MD5sum: a8c02c3af86ebc0916bae80c64419b18 NeedsCompilation: no Package: clusterSeq Version: 1.8.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: f82bb977baa0ce56344f8732a4fbdca0 NeedsCompilation: no Package: ClusterSignificance Version: 1.12.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: b97eb45eafae8a055983244ffd40d33a NeedsCompilation: no Package: clusterStab Version: 1.56.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: d55549ed704e0e7d13c80c9d6a13b1b2 NeedsCompilation: no Package: CMA Version: 1.42.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: a1fd257a7b975dd6c6c31b60dd072e36 NeedsCompilation: no Package: cn.farms Version: 1.32.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: fb0b30634c95a67c17e7b8f652c0b1a3 NeedsCompilation: yes Package: cn.mops Version: 1.30.0 Depends: R (>= 2.12), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors, exomeCopy Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 503588f63a7ee549f7bb6f001b147cb5 NeedsCompilation: yes Package: CNAnorm Version: 1.30.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 30e28ca6bb87d15fa7c5a6f464f4f55e NeedsCompilation: yes Package: CNEr Version: 1.20.0 Depends: R (>= 3.4) Imports: Biostrings (>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: cf1a825dd6ed04ab61022de008fd5535 NeedsCompilation: yes Package: CNORdt Version: 1.26.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 4de4604fc7299bfdab6568b3bc769da1 NeedsCompilation: yes Package: CNORfeeder Version: 1.24.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph License: GPL-3 MD5sum: 2d7828bfb2c79b93ed53013e0d0f1fff NeedsCompilation: no Package: CNORfuzzy Version: 1.26.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: e309f6b2e672b473f696368fd2a62595 NeedsCompilation: yes Package: CNORode Version: 1.26.0 Depends: CellNOptR (>= 1.5.14), genalg Enhances: MEIGOR License: GPL-2 MD5sum: 800cc2ee0114d43e824ce48573f517d0 NeedsCompilation: yes Package: CNPBayes Version: 1.13.5 Depends: R (>= 3.4.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.1), S4Vectors, matrixStats, RColorBrewer, gtools, combinat, GenomeInfoDb (>= 1.11.6), methods, BiocGenerics, graphics, stats, coda, SummarizedExperiment, mclust, reshape2, ggplot2, magrittr, purrr, tidyr, dplyr, tibble, scales, data.table, RcppArmadillo LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS, VanillaICE, tidyverse License: Artistic-2.0 MD5sum: 8e50d11d4d4152779c2f999901665d93 NeedsCompilation: yes Package: CNTools Version: 1.40.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: d3fab8b1e26b17398d947fb7785b06f5 NeedsCompilation: yes Package: cnvGSA Version: 1.28.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: c0795147bf7c9c04734e76a4a9d5ad28 NeedsCompilation: no Package: CNVPanelizer Version: 1.16.0 Depends: R (>= 3.2.0), GenomicRanges Imports: S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: cb6a6ddd87aff3639c36971aa6260251 NeedsCompilation: no Package: CNVRanger Version: 1.0.3 Depends: GenomicRanges, RaggedExperiment Imports: BiocParallel, GDSArray, GenomeInfoDb, Gviz, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown License: Artistic-2.0 MD5sum: 39d0c51f24064a85b0045803d6ae3b76 NeedsCompilation: no Package: CNVrd2 Version: 1.22.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 4794f092465ee552756f69506e6a0b93 NeedsCompilation: no Package: CNVtools Version: 1.78.0 Depends: R (>= 2.10), survival License: GPL-3 MD5sum: f9844ca1cd5bb736dc47736f3848b3e4 NeedsCompilation: yes Package: cobindR Version: 1.22.0 Imports: methods, seqinr, yaml, rtfbs, gplots, mclust, gmp, BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome, biomaRt Suggests: RUnit Enhances: rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall License: Artistic-2.0 MD5sum: 435e9185e8656279a82919a21d95a5fd NeedsCompilation: no Package: CoCiteStats Version: 1.56.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 4b07800c4a99cf17a31094fd78d7ce6e NeedsCompilation: no Package: COCOA Version: 1.2.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 2a3284970a78abe427089c9bc74f4076 NeedsCompilation: no Package: codelink Version: 1.52.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: b7c747213e454bfb4f6f8191815d36ec NeedsCompilation: no Package: CODEX Version: 1.16.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: a17ebe2c29dccb53f92d0417d22f2363 NeedsCompilation: no Package: coexnet Version: 1.6.0 Depends: R (>= 3.4) Imports: affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown Suggests: RUnit, BiocGenerics, knitr License: LGPL MD5sum: 2dc427a31e354e132cf875cf6378ed8f NeedsCompilation: no Package: CoGAPS Version: 3.4.1 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, data.table, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5 LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (== 2) MD5sum: 636b3400784dc545307e18ff215c12ff NeedsCompilation: yes Package: cogena Version: 1.18.0 Depends: R (>= 3.5.0), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, dplyr, devtools Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: b785e1765e816c29bfaeb53b57fdf454 NeedsCompilation: no Package: coGPS Version: 1.28.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 49800c742e5b6176809de49f5a58a938 NeedsCompilation: no Package: COHCAP Version: 1.30.0 Depends: WriteXLS, COHCAPanno, RColorBrewer, gplots Imports: Rcpp, RcppArmadillo, BH LinkingTo: Rcpp, BH License: GPL-3 MD5sum: 8009dc2a7a0bf2f7bdaee07a0802496b NeedsCompilation: yes Package: cola Version: 1.0.1 Depends: R (>= 3.6.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.0.0), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr, markdown, digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), data.tree, dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, AnnotationDbi, gplots License: MIT + file LICENSE MD5sum: f2cfa5439c1b799e710ca70eb087a7e3 NeedsCompilation: yes Package: coMET Version: 1.16.0 Depends: R (>= 3.6.0), grid, utils, biomaRt, Gviz, psych Imports: colortools, hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: bd89b930a424c677834857e55b7237f3 NeedsCompilation: no Package: compartmap Version: 1.2.0 Depends: R (>= 3.5.0), minfi, Homo.sapiens, mixOmics Imports: SummarizedExperiment, GenomicRanges, gtools, parallel Suggests: covr, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 3a5b9a72c01eaef3aafd6f7e8124e83c NeedsCompilation: no Package: COMPASS Version: 1.22.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2 License: Artistic-2.0 MD5sum: f3efd33af8043c6ec9b8e668e645e2a5 NeedsCompilation: yes Package: compcodeR Version: 1.20.1 Depends: R (>= 3.0.2), sm Imports: tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0) Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: f8b53fb87689d48230039718ab8b87d1 NeedsCompilation: no Package: compEpiTools Version: 1.18.0 Depends: R (>= 3.1.1), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 5634de2c34a8a8006e7025d34234797e NeedsCompilation: no Package: CompGO Version: 1.20.0 Depends: RDAVIDWebService Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview License: GPL-2 MD5sum: f5dd5a91ff4f0dec75db80fddf3731f5 NeedsCompilation: no Package: ComplexHeatmap Version: 2.0.0 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges License: MIT + file LICENSE MD5sum: 9c18a94275f005a74bf2d7e5a30ff3ea NeedsCompilation: no Package: condcomp Version: 1.1.1 Depends: R (>= 3.5.0) Imports: cluster, ggplot2, ggrepel, outliers Suggests: testthat, knitr, rmarkdown, BiocStyle, Matrix, Seurat, monocle, HSMMSingleCell License: GPL (>= 2) | file LICENSE MD5sum: 0f1919283cb85a0552f82365b33d193e NeedsCompilation: no Package: CONFESS Version: 1.12.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: 9d796e40ddb6520234e5a68e3bbb7d2b NeedsCompilation: no Package: consensus Version: 1.2.2 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: ab89787df7f89f06fe59e4114a7c6f97 NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.48.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 866829344d197d481e17c6101abd0856 NeedsCompilation: no Package: consensusDE Version: 1.2.1 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 9e18073efbd56789ff5da4299ace0074 NeedsCompilation: no Package: consensusOV Version: 1.6.0 Depends: R (>= 3.4) Imports: Biobase, GSVA, gdata, genefu, limma, matrixStats, randomForest, stats, utils Suggests: knitr, ggplot2 License: Artistic-2.0 MD5sum: edacb8fa98a32c5388bfed32307b3496 NeedsCompilation: no Package: consensusSeekeR Version: 1.12.0 Depends: R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: ddf046f4b7cc24ef7da7f0172594de24 NeedsCompilation: no Package: contiBAIT Version: 1.12.0 Depends: BH (>= 1.51.0-3), Rsamtools (>= 1.21) Imports: data.table, grDevices, clue, cluster, gplots, IRanges, GenomicRanges, S4Vectors, Rcpp, TSP, GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods, exomeCopy, GenomicAlignments, diagram LinkingTo: Rcpp, BH Suggests: BiocStyle License: BSD_2_clause + file LICENSE MD5sum: d6a506be45a84ec08ecd8a6434d47fc8 NeedsCompilation: yes Package: conumee Version: 1.18.0 Depends: R (>= 3.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: 19965541916026a8a1ddd80627772222 NeedsCompilation: no Package: convert Version: 1.60.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: f4e2775a7a35742a6ce8265d2156a2d9 NeedsCompilation: no Package: copa Version: 1.52.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: ebc47c86e5c884013d3b4f0fd4366c42 NeedsCompilation: yes Package: copynumber Version: 1.24.0 Depends: R (>= 2.10), BiocGenerics Imports: S4Vectors, IRanges, GenomicRanges License: Artistic-2.0 MD5sum: 465a840dd46f78b16e9eb8f9b2d31865 NeedsCompilation: no Package: CopyNumberPlots Version: 1.0.1 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, utils Suggests: BiocStyle, knitr, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy License: Artistic-2.0 MD5sum: 1897a7b069665e5d40019ba315ab42c5 NeedsCompilation: no Package: CopywriteR Version: 2.16.0 Depends: R(>= 3.2), BiocParallel Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger Suggests: BiocStyle, SCLCBam, snow License: GPL-2 MD5sum: b3ff89f23a907740463bf7282689f384 NeedsCompilation: no Package: coRdon Version: 1.2.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 9fbd4bba3bbbd8fb23a683170a77cf0f NeedsCompilation: no Package: CoRegFlux Version: 1.0.0 Depends: R (>= 3.6) Imports: CoRegNet, sybil Suggests: glpkAPI, testthat, knitr, rmarkdown, digest, R.cache, ggplot2, plyr, igraph, methods, latex2exp, rBayesianOptimization License: GPL-3 MD5sum: 1166cd531721136b6d1825bc83c82cbd NeedsCompilation: no Package: CoRegNet Version: 1.22.0 Depends: R (>= 2.14), igraph, shiny, arules, methods Suggests: RColorBrewer, gplots, BiocStyle, knitr License: GPL-3 MD5sum: 15562e61d7856a361e519160696701e1 NeedsCompilation: yes Package: Cormotif Version: 1.30.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: f2fb657c778e48018575f928a729f606 NeedsCompilation: no Package: CorMut Version: 1.26.0 Depends: methods,seqinr,igraph License: GPL-2 MD5sum: 7b38f2d9cd75e9410e2cce41b0b45f40 NeedsCompilation: no Package: CORREP Version: 1.50.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) MD5sum: 337c57abb391e1b24492671e8e479594 NeedsCompilation: no Package: coseq Version: 1.8.0 Depends: R (>= 3.4.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2 (>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8), grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: ca85966ba23706ba1f3ce752d4c43a17 NeedsCompilation: no Package: cosmiq Version: 1.18.0 Depends: R (>= 3.0.2), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 7280905e37ca78bd4d6557311fe07d18 NeedsCompilation: yes Package: COSNet Version: 1.18.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5db1fd2a292bb507438470c11477910c NeedsCompilation: yes Package: CountClust Version: 1.12.0 Depends: R (>= 3.4), ggplot2 (>= 2.1.0) Imports: SQUAREM, slam, maptpx, plyr(>= 1.7.1), cowplot, gtools, flexmix, picante, limma, parallel, reshape2, stats, utils, graphics, grDevices Suggests: knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable License: GPL (>= 2) MD5sum: b9aa36dedfc2a7fb087e027e2e40d7bf NeedsCompilation: no Package: countsimQC Version: 1.2.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 0.9.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 0cff7db1e83c85c84ad72f5e24fac4ef NeedsCompilation: no Package: covEB Version: 1.10.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: d936d0ebb4fe7540db44a8d77c60f770 NeedsCompilation: no Package: CoverageView Version: 1.22.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 3713144fc6a492d347e4d0088705dd06 NeedsCompilation: no Package: covRNA Version: 1.10.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 45420d33aa33dc000e6d93bd9631c602 NeedsCompilation: no Package: cpvSNP Version: 1.16.0 Depends: R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: fe5f5b8dd0f39d5fec228b88b0a702a4 NeedsCompilation: no Package: cqn Version: 1.30.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 3cdf1037d31884fe295ff7ab0bdc68da NeedsCompilation: no Package: CRImage Version: 1.32.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 7ace556d1951e5c55d93d081953153a2 NeedsCompilation: no Package: CRISPRseek Version: 1.24.0 Depends: R (>= 3.0.1), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, BiocParallel, hash Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: 9dbb4cffe40d991680210919a4db879d NeedsCompilation: no Package: crisprseekplus Version: 1.10.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 14baca0d404914db60ec75a333550e12 NeedsCompilation: no Package: CrispRVariants Version: 1.12.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: ef9f95207557f57a1c1818c45a21eb7b NeedsCompilation: no Package: crlmm Version: 1.42.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit License: Artistic-2.0 MD5sum: 73c3522b65b499db015b7027fd1d349f NeedsCompilation: yes Package: crossmeta Version: 1.10.0 Depends: R (>= 3.5) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), ccmap, DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), doParallel (>= 1.0.10), doRNG (>= 1.6), foreach (>= 1.4.3), fdrtool (>= 1.2.15), ggplot2 (>= 2.2.1), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), metap (>= 0.8), miniUI (>= 0.1.1), oligo (>= 1.38.0), plotly(>= 4.5.6), reshape (>= 0.8.6), reader(>= 1.0.6), RColorBrewer (>= 1.1.2), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), rdrop2 (>= 0.7.0), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), stats (>= 3.3.3), XML (>= 3.98.1.17), Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata License: MIT + file LICENSE MD5sum: a7e2ea603db3fedc20fb7783003eeedb NeedsCompilation: no Package: CSAR Version: 1.36.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: a7187a296ff5f634727e0d4d8c277b6f NeedsCompilation: yes Package: csaw Version: 1.18.0 Depends: GenomicRanges, SummarizedExperiment Imports: Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 9bd64f602a67ea5a18eabc7ecef5d031 NeedsCompilation: yes Package: CSSP Version: 1.22.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 MD5sum: 0df8f08ebb21ddcea13f1b3a096f28dc NeedsCompilation: yes Package: ctc Version: 1.58.0 Depends: amap License: GPL-2 MD5sum: 8c4c2f9b987498ff1fe4f73d0354ae23 NeedsCompilation: no Package: CTDquerier Version: 1.4.0 Depends: R (>= 3.4.0) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache, rappdirs Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: b17b3506564035fe23a6e0e92d163fac NeedsCompilation: no Package: cTRAP Version: 1.2.0 Depends: R (>= 3.5.0) Imports: data.table, limma, stats, fgsea, pbapply, plyr, cowplot, ggplot2, rhdf5, R.utils, httr, methods, piano, readr, utils, graphics Suggests: testthat, knitr, covr, biomaRt License: MIT + file LICENSE MD5sum: a3b7c8688824fa8c631f6675c0438dd2 NeedsCompilation: no Package: ctsGE Version: 1.10.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: 82dbb0de98157d7ddc1ecde7ed463bdc NeedsCompilation: no Package: cummeRbund Version: 2.26.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: 9d6f7bf9e12be69be7391f2f369f9f0d NeedsCompilation: no Package: customProDB Version: 1.24.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: f0480be5b51b492ef68898710c8c56aa NeedsCompilation: no Package: CVE Version: 1.10.0 Depends: R (>= 3.4.0), tidyverse, plyr, ggplot2 Imports: shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite, ape, WGCNA Suggests: knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle License: GPL-3 MD5sum: 2396cfaf7ce6b60195a6af560d5c1d66 NeedsCompilation: no Package: cycle Version: 1.38.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 2cd209230387fc9f0631f2d0e1fcd46a NeedsCompilation: no Package: cydar Version: 1.8.0 Depends: BiocParallel, SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp, BiocNeighbors, SummarizedExperiment LinkingTo: Rcpp Suggests: ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: ce5632a0901f34dd03c93f5d6389a375 NeedsCompilation: yes Package: CytoDx Version: 1.4.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr License: GPL-2 MD5sum: 28c899b94fb5cac16103e4cd83d76037 NeedsCompilation: no Package: cytofast Version: 1.0.0 Depends: R (>= 3.6.0) Imports: flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats, grDevices, Rdpack, methods, grid, FlowSOM Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 4400b4f61df017e6f5a9f902d39da411 NeedsCompilation: no Package: cytolib Version: 1.6.0 Depends: R (>= 3.4) LinkingTo: BH(>= 1.62.0-1), RProtoBufLib(>= 1.1.7) Suggests: knitr License: Artistic-2.0 MD5sum: b485d248ce7346c0beafaff56d68dcd7 NeedsCompilation: no Package: CytoML Version: 1.10.0 Imports: flowCore (>= 1.43.10), flowWorkspace (>= 3.31.17), openCyto (>= 1.11.3), XML, data.table, flowUtils (>= 1.35.7), jsonlite, RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, lattice LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel Suggests: testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel License: Artistic-2.0 MD5sum: 9b02fad08a21f76fc73cc24fff7211b1 NeedsCompilation: yes Package: dada2 Version: 1.12.1 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-3 MD5sum: ef5237a23b1cc04f92de1d1faac213d9 NeedsCompilation: yes Package: dagLogo Version: 1.22.3 Depends: R (>= 3.0.1), methods, biomaRt, grImport2, grid, motifStack Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils Suggests: XML, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 4698ebcd4cb0becc9055c3392db1329b NeedsCompilation: no Package: daMA Version: 1.56.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 062d03b002e2ef63716ffbc7d709c9dd NeedsCompilation: no Package: DaMiRseq Version: 1.8.0 Depends: R (>= 3.4), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 39e1c34e6e3b181a85b1a4ed9f7324f4 NeedsCompilation: no Package: DAPAR Version: 1.16.11 Depends: R (>= 3.6), foreach, parallel, doParallel Imports: MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png, lattice,reshape2,gplots,pcaMethods,ggplot2, limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics, openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot, imp4p (>= 0.8), highcharter (>= 0.5.0), DAPARdata (>= 1.11.2), siggenes, graph, lme4, readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra Suggests: BiocGenerics, Biobase, testthat, BiocStyle License: Artistic-2.0 MD5sum: ddac8950abeaeddebf9a145362703668 NeedsCompilation: no Package: DART Version: 1.32.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 3e0b9ba160194b3200963009133620ba NeedsCompilation: no Package: DBChIP Version: 1.28.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) MD5sum: 8a7945a976f67ca5f9a0e0416c25f485 NeedsCompilation: no Package: dcanr Version: 1.0.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 3d8ea0c3dd1aec60c5f1cb87bd55cbd3 NeedsCompilation: no Package: dcGSA Version: 1.12.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: e0657f2cdbcd15aed33108d311ffc6f6 NeedsCompilation: no Package: DChIPRep Version: 1.14.0 Depends: R (>= 3.4), DESeq2 Imports: methods, stats, utils, ggplot2, fdrtool, reshape2, GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr, assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENCE MD5sum: f2de5544bb683f3c476ac945450a0ac7 NeedsCompilation: no Package: ddCt Version: 1.40.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 MD5sum: b211d12a2de05a10f8fa66d8449b8522 NeedsCompilation: no Package: ddPCRclust Version: 1.4.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: aab48e900fbc6ea52c57c297b0850f62 NeedsCompilation: no Package: debrowser Version: 1.12.3 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 5156d25ce4e864350b75121e23953c82 NeedsCompilation: no Package: DECIPHER Version: 2.12.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 0bcfc1d4493c22bc9287d6b4525a6f73 NeedsCompilation: yes Package: deco Version: 1.0.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens License: GPL (>= 3) MD5sum: c0f8d851c4d54bbb75d233024b60c2e5 NeedsCompilation: no Package: DEComplexDisease Version: 1.4.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 MD5sum: 513c04ff3be9a08ec70f54c148c44879 NeedsCompilation: yes Package: decompTumor2Sig Version: 2.0.0 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: a1ad320d7db408fc59c16dfc97b0578d NeedsCompilation: no Package: DeconRNASeq Version: 1.26.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: e5ef95e4fa67c3af0692a3fc2fbd4f64 NeedsCompilation: no Package: decontam Version: 1.4.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: ac1669c915a51167c800d83b008ad20c NeedsCompilation: no Package: DEDS Version: 1.58.0 Depends: R (>= 1.7.0) License: LGPL MD5sum: 7ac7e8cf17dab9cd14df45cd2beb9fe8 NeedsCompilation: yes Package: DeepBlueR Version: 1.10.0 Depends: R (>= 3.3), XML, RCurl Imports: GenomicRanges, data.table, stringr, diffr, dplyr, methods, rjson, utils, R.utils, foreach, withr, rtracklayer, GenomeInfoDb, settings, filehash Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats License: GPL (>= 2.0) MD5sum: 40b7e1b2d6736d0ce796bfad122568c4 NeedsCompilation: no Package: deepSNV Version: 1.30.0 Depends: R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 2547a2cad930d74948b182b285df1c07 NeedsCompilation: yes Package: DEFormats Version: 1.12.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: 5d280ee04668d89bdf8065b18451f7aa NeedsCompilation: no Package: DEGraph Version: 1.36.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: 29e1cfa7fe5e9ea44f6ac99e847e9fde NeedsCompilation: no Package: DEGreport Version: 1.20.0 Depends: R (>= 3.5.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: d46192672effa5839311e532c523465f NeedsCompilation: no Package: DEGseq Version: 1.38.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 6c69744cb13c43d7a0d91bb0b045c5b0 NeedsCompilation: yes Package: DelayedArray Version: 0.10.0 Depends: R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3), BiocParallel Imports: stats, Matrix LinkingTo: S4Vectors Suggests: Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 7ae9f998c8c10a0807dd4fc56c6c90c9 NeedsCompilation: yes Package: DelayedDataFrame Version: 1.0.0 Depends: R (>= 3.6), S4Vectors (>= 0.19.12), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 MD5sum: 60d192f4f76c29989e1feb0e47d23660 NeedsCompilation: no Package: DelayedMatrixStats Version: 1.6.1 Depends: DelayedArray (>= 0.9.8) Imports: methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem License: MIT + file LICENSE MD5sum: e10e9ab312eafd0e6344c7f622b1f08c NeedsCompilation: no Package: deltaGseg Version: 1.24.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 05b04ca791d4530c8edd16df31f2a2c4 NeedsCompilation: no Package: DeMAND Version: 1.14.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 2dbb15daf66fb5efe935fee33d49fd7b NeedsCompilation: no Package: DeMixT Version: 1.0.4 Depends: R (>= 3.6), parallel, SummarizedExperiment, knitr, KernSmooth Imports: matrixStats, stats License: GPL-3 MD5sum: c46c5dfb72ac72c405e4e48185a23c8e NeedsCompilation: yes Package: DEP Version: 1.6.1 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 442b4f740e4512824c8cd0122180373e NeedsCompilation: no Package: DepecheR Version: 1.0.3 Depends: R (>= 3.6) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), BiocParallel (>= 1.16.6) LinkingTo: Rcpp, RcppEigen Suggests: Rtsne, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 59782a5b2177682de7a2d7c94365d92f NeedsCompilation: yes Package: DEqMS Version: 1.2.0 Depends: R(>= 3.5),graphics,stats,ggplot2,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 06cffbc05f01e49b60ca5cadfe31bc04 NeedsCompilation: no Package: derfinder Version: 1.18.9 Depends: R(>= 3.2) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.9.38), stats Suggests: BiocStyle (>= 2.5.19), biovizBase, sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: ac8d35fc10110904b4d6f523797224d7 NeedsCompilation: no Package: derfinderHelper Version: 1.18.1 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat License: Artistic-2.0 MD5sum: 85a1b2f0c51e5caca083f6fc1a14d14c NeedsCompilation: no Package: derfinderPlot Version: 1.18.1 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, RefManageR, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 17d48caee038d128667eb5e94ced3bb5 NeedsCompilation: no Package: DEScan2 Version: 1.4.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors, SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: 601fc7fa0c23f543e35db969282faea5 NeedsCompilation: yes Package: DESeq Version: 1.36.0 Depends: BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice Imports: genefilter, geneplotter, methods, MASS, RColorBrewer Suggests: pasilla (>= 0.2.10), vsn, gplots License: GPL (>= 3) MD5sum: 2f4ef93911b4e75bc0b470bb0b9d70d0 NeedsCompilation: yes Package: DESeq2 Version: 1.24.0 Depends: S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) License: LGPL (>= 3) MD5sum: 51a2fd660c9f615e5819e795b62c125e NeedsCompilation: yes Package: DEsingle Version: 1.4.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: f9d286f5314f05cf0ac1f38da3a691ad NeedsCompilation: no Package: destiny Version: 2.14.0 Depends: R (>= 3.3.0) Imports: methods, graphics, grDevices, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, Biobase, BiocGenerics, SummarizedExperiment, ggplot2, ggthemes, VIM, proxy, igraph, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: nbconvertR, testthat, FNN, tidyr, SingleCellExperiment Enhances: rgl, SingleCellExperiment License: GPL MD5sum: 4b2e28a4eb7022cfad8589c8c6d45ded NeedsCompilation: yes Package: DEsubs Version: 1.10.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 3401c12e1b7b956a302c894862bbff72 NeedsCompilation: no Package: DEXSeq Version: 1.30.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 756246353a1779eebec78015ca33d881 NeedsCompilation: no Package: dexus Version: 1.24.0 Depends: R (>= 2.15), methods, BiocGenerics Imports: stats Suggests: parallel, statmod, DESeq, RColorBrewer License: LGPL (>= 2.0) MD5sum: cb34d5e04455977ed9a0bd3d0f275c1c NeedsCompilation: yes Package: DFP Version: 1.42.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: 2101788ecc7a5ee2507bfb52ade1a716 NeedsCompilation: no Package: DiffBind Version: 2.12.0 Depends: R (>= 3.5), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, edgeR, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 1.99.1), DESeq2, methods, graphics, ggrepel LinkingTo: Rhtslib (>= 1.15.3), Rcpp Suggests: DESeq, BiocStyle, testthat Enhances: rgl, XLConnect License: Artistic-2.0 MD5sum: ae0905af5e87e5525769294d162ef611 NeedsCompilation: yes Package: diffcoexp Version: 1.4.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery License: GPL (> 2) MD5sum: 49a4bd12fa99f28a09013c7e2dbd9fd5 NeedsCompilation: no Package: diffcyt Version: 1.4.4 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 0f1d14ddce48460a3df47f42d9231391 NeedsCompilation: no Package: diffGeneAnalysis Version: 1.66.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: fba381a248d6938a6eb4eae857a11d76 NeedsCompilation: no Package: diffHic Version: 1.16.0 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: 1b82b5c50751576e1e81fdc2493d7b64 NeedsCompilation: yes Package: DiffLogo Version: 2.8.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: dcc3efcb7888d29382b8aee7dc141c8e NeedsCompilation: no Package: diffloop Version: 1.12.0 Imports: methods, GenomicRanges, foreach, plyr, dplyr, reshape2, ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt, GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats, utils, Biobase, readr, data.table, rtracklayer, pbapply, limma Suggests: DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 9d151ba0bf75463de9f3b0d13d96b5dc NeedsCompilation: no Package: diffuStats Version: 1.4.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2 License: GPL-3 MD5sum: 2d28196f508d79d81d396b315e840fa8 NeedsCompilation: yes Package: diggit Version: 1.16.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: 03554cd853612f596c1c3d7abbd93ba4 NeedsCompilation: no Package: Director Version: 1.10.0 Depends: R (>= 3.3) Imports: htmltools, utils, grDevices License: GPL-3 + file LICENSE MD5sum: 531b8d69150abadd2afb8c87c6f7929a NeedsCompilation: no Package: DirichletMultinomial Version: 1.26.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 MD5sum: ff77746ada0149b0fb99d375f17c4b4d NeedsCompilation: yes Package: discordant Version: 1.8.0 Depends: R (>= 3.4) Imports: Biobase, stats, biwt, gtools, MASS, tools Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 59e96c19225caa973d164391632985a2 NeedsCompilation: yes Package: DiscoRhythm Version: 1.0.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors Suggests: testthat License: GPL-3 MD5sum: 850593d2b075f4bae3be34fad5eb7727 NeedsCompilation: no Package: divergence Version: 1.0.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 4aa6ee4b37d749a4349d8da511e87cee NeedsCompilation: no Package: dks Version: 1.30.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 01287b09c7acdd4a20edba7351bdb187 NeedsCompilation: no Package: DMCHMM Version: 1.6.0 Depends: R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool Imports: utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics Suggests: testthat, knitr License: GPL-3 MD5sum: 4b451c76bb34a68bc240b018e31eec15 NeedsCompilation: no Package: DMRcaller Version: 1.16.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 23001b628eb991beec5ef7ad3921f1b1 NeedsCompilation: no Package: DMRcate Version: 1.20.0 Depends: R (>= 3.3.0), minfi, DSS, DMRcatedata Imports: limma, missMethyl, GenomicRanges, parallel, methods, graphics, plyr, Gviz, IRanges, stats, utils, S4Vectors Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: file LICENSE MD5sum: 835c193be0468ad25fb4eb90bda45c77 NeedsCompilation: no Package: DMRforPairs Version: 1.20.0 Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel License: GPL (>= 2) MD5sum: 4f92ad08fcb9bdbd584cac54e4ed788c NeedsCompilation: no Package: DMRScan Version: 1.10.0 Depends: R (>= 3.4.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb, methods, mvtnorm, stats, parallel Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: b5ecc41efedcac307eea126809b029a4 NeedsCompilation: no Package: dmrseq Version: 1.4.9 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 91a6080d1836ee9341b3bf0f5f7c45f1 NeedsCompilation: no Package: DNABarcodeCompatibility Version: 1.0.2 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats, utils, methods Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: b3965fd4f3fe965c79ac6ca2fa5bb0d1 NeedsCompilation: no Package: DNABarcodes Version: 1.14.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: d5e24b79f158ae0aa4641b8215e81f7c NeedsCompilation: yes Package: DNAcopy Version: 1.58.0 License: GPL (>= 2) MD5sum: 459165b252a246b8cfe1b1dc792079c8 NeedsCompilation: yes Package: DNAshapeR Version: 1.12.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: 7f27913e977cf523165f72f81957c94e NeedsCompilation: yes Package: DominoEffect Version: 1.4.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges Suggests: knitr, testthat License: GPL (>= 3) MD5sum: 72e2fad413e30de2ff92289505bebbb7 NeedsCompilation: no Package: doppelgangR Version: 1.12.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy License: GPL (>= 2.0) MD5sum: e592f39c775f1c9ab21a45f3b9261c6d NeedsCompilation: no Package: DOQTL Version: 1.19.0 Depends: R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, VariantAnnotation Imports: annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators, mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML Suggests: MUGAExampleData License: GPL-3 MD5sum: 680f81e25019ae46bc2eb0ea51bdd72e NeedsCompilation: yes Package: Doscheda Version: 1.6.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, d3heatmap, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6f97a7a6534ee3d3c09d0c35e23e71d8 NeedsCompilation: no Package: DOSE Version: 3.10.2 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils Suggests: prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat License: Artistic-2.0 MD5sum: 282e75af7ce19d94fd035777fb196829 NeedsCompilation: no Package: doseR Version: 1.0.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 66d789556a8eadf0bc626496ca65b490 NeedsCompilation: no Package: drawProteins Version: 1.4.0 Depends: R (>= 3.4) Imports: ggplot2, httr, dplyr, readr, stringr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cea2f328f8d1343ea7c79eb07a7c0774 NeedsCompilation: no Package: DRIMSeq Version: 1.12.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 399bc7fe47de2da27d0f357470c7037e NeedsCompilation: no Package: DriverNet Version: 1.24.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: 5fa9c7883dd6b274a3e22bc1e4b25678 NeedsCompilation: no Package: DropletUtils Version: 1.4.3 Depends: SingleCellExperiment Imports: S4Vectors, BiocParallel, Rcpp, Matrix, methods, utils, stats, edgeR, rhdf5, HDF5Array, R.utils, dqrng LinkingTo: Rcpp, beachmat, Rhdf5lib, BH, dqrng Suggests: testthat, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 8776eefde77ae70d76915b4f9d4ba017 NeedsCompilation: yes Package: DrugVsDisease Version: 2.26.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable License: GPL-3 MD5sum: 548b0dc940cdc16bec2d6b9d610d463c NeedsCompilation: no Package: DSS Version: 2.32.0 Depends: R (>= 3.3), Biobase, bsseq, splines, methods Imports: stats, graphics, DelayedArray Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 24e4aa2a0263452f0a28e93a660789f1 NeedsCompilation: yes Package: DTA Version: 2.30.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: e4fe6eb840110181a531da530d2ddee4 NeedsCompilation: no Package: dualKS Version: 1.44.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods Imports: graphics License: LGPL (>= 2.0) MD5sum: 8179aa4020d4188a630cccc07313bc4e NeedsCompilation: no Package: DupChecker Version: 1.22.0 Imports: tools, R.utils, RCurl Suggests: knitr License: GPL (>= 2) MD5sum: f9c7509c929ec424905a344d2a4bf81e NeedsCompilation: no Package: dupRadar Version: 1.14.0 Depends: R (>= 3.2.0) Imports: Rsubread (>= 1.14.1) Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub License: GPL-3 MD5sum: f97053380896eef28891a1ea2f6fca70 NeedsCompilation: no Package: dyebias Version: 1.44.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 MD5sum: 2f434cc8b244800f94d4301d29ae1b25 NeedsCompilation: no Package: DynDoc Version: 1.62.0 Depends: methods, utils Imports: methods License: Artistic-2.0 MD5sum: 3e9372cbe7a1d407f48e62f87e984c1b NeedsCompilation: no Package: EasyqpcR Version: 1.26.0 Imports: plyr, matrixStats, plotrix, gWidgetsRGtk2 Suggests: SLqPCR, qpcrNorm, qpcR, knitr License: GPL (>= 2) MD5sum: f1bfda9188d2d66721b5035c0bd4bd46 NeedsCompilation: no Package: easyRNASeq Version: 2.20.0 Imports: Biobase (>= 2.41.2), BiocFileCache (>= 1.7.10), BiocGenerics (>= 0.27.1), BiocParallel (>= 1.15.15), biomaRt (>= 2.37.9), Biostrings (>= 2.49.2), DESeq (>= 1.33.0), edgeR (>= 3.23.6), GenomeInfoDb (>= 1.17.4), genomeIntervals (>= 1.37.0), GenomicAlignments (>= 1.17.3), GenomicRanges (>= 1.33.14), SummarizedExperiment (>= 1.11.6), graphics, IRanges (>= 2.15.18), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 1.33.7), S4Vectors (>= 0.19.23), ShortRead (>= 1.39.0), utils Suggests: BiocStyle (>= 2.9.6), BSgenome (>= 1.49.5), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) License: Artistic-2.0 MD5sum: 7db78c0f10e0bac811550c80ae29c372 NeedsCompilation: no Package: EBarrays Version: 2.48.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: 608cdd3e7a7efa9de797cc7cd8076e2a NeedsCompilation: yes Package: EBcoexpress Version: 1.28.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: 9a21fccfdac28510fb2cf51bae19638d NeedsCompilation: yes Package: EBImage Version: 4.26.0 Depends: methods Imports: BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: 098cfb9ab5b7d4f10ad9cbba2bf6a3cb NeedsCompilation: yes Package: EBSEA Version: 1.12.0 Imports: edgeR, limma, graphics, stats, plyr License: GPL-2 MD5sum: fd19e2b5af8e9eb07c0991802c63068c NeedsCompilation: no Package: EBSeq Version: 1.24.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) License: Artistic-2.0 MD5sum: becd6c60c5358cfc63ca19c6ce33f87c NeedsCompilation: no Package: EBSeqHMM Version: 1.18.0 Depends: EBSeq License: Artistic-2.0 MD5sum: 8f2f866cd05535d159b93b39e59c7ce5 NeedsCompilation: no Package: ecolitk Version: 1.56.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: d7eeb11fad631ce3934581f5f7606aeb NeedsCompilation: no Package: EDASeq Version: 2.18.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq, aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat License: Artistic-2.0 MD5sum: 478a1ed2c78ff2d606de4fae097f6776 NeedsCompilation: no Package: EDDA Version: 1.22.0 Depends: Rcpp (>= 0.10.4),parallel,methods,ROCR,DESeq,baySeq,snow,edgeR Imports: graphics, stats, utils, parallel, methods, ROCR, DESeq, baySeq, snow, edgeR LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 644dc53ad78a4e34f618d4f76ef7a04f NeedsCompilation: yes Package: edge Version: 2.16.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, snm, jackstraw, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: 48cb021c6bd3677e96f44d419ef4382f NeedsCompilation: yes Package: edgeR Version: 3.26.8 Depends: R (>= 3.6.0), limma (>= 3.34.5) Imports: graphics, stats, utils, methods, locfit, Rcpp LinkingTo: Rcpp Suggests: AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines License: GPL (>= 2) MD5sum: 3e91d0c8be574095017c58f670cced4e NeedsCompilation: yes Package: eegc Version: 1.10.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 MD5sum: b05f2f7a3f6e39f65f1deea5ee9e874d NeedsCompilation: no Package: EGAD Version: 1.12.0 Depends: R(>= 3.3) Imports: gplots, Biobase, GEOquery, limma, arrayQualityMetrics, impute, RColorBrewer, zoo, igraph, plyr, Matrix, MASS, RCurl, affy Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 51baa1af3e40ef6ac8b84484d61c8091 NeedsCompilation: no Package: EGSEA Version: 1.12.0 Depends: R (>= 3.5), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), Glimma (>= 1.4.0), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 74eecf4e7b394954f7616a2fe86d926e NeedsCompilation: no Package: eiR Version: 1.24.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, gespeR,RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap License: Artistic-2.0 MD5sum: aa753e91c09aeb6f53c66957e36d7d99 NeedsCompilation: yes Package: eisa Version: 1.36.0 Depends: isa2, Biobase (>= 2.17.8), AnnotationDbi, methods Imports: BiocGenerics, Category, genefilter, DBI Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) MD5sum: cf034edc59e97a5ba8fd5322bc36c876 NeedsCompilation: no Package: ELBOW Version: 1.20.0 Depends: R (>= 2.15.0) Imports: graphics, stats, utils Suggests: DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer, hgu133plus2cdf, hgu133plus2probe License: file LICENSE License_is_FOSS: yes License_restricts_use: no MD5sum: a7f6650044af31c238c8d98c0d56e437 NeedsCompilation: no Package: ELMER Version: 2.8.3 Depends: R (>= 3.4.0), ELMER.data (>= 2.8.1) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.9.2), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, ggpubr, rtracklayer, DelayedArray Suggests: BiocStyle, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr License: GPL-3 MD5sum: 15ece23016572be0d4bfb446e11f3550 NeedsCompilation: no Package: EMDomics Version: 2.14.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: baabbdfdbaf4306ac2d89804857133a0 NeedsCompilation: no Package: EmpiricalBrownsMethod Version: 1.12.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e4b0403a9ba17adcf61cba37e292cf0f NeedsCompilation: no Package: ENCODExplorer Version: 2.10.0 Depends: R (>= 3.6), shiny, DT, shinythemes Imports: tools, jsonlite, RCurl, tidyr, data.table, dplyr, stringr, stringi, utils, AnnotationHub Suggests: RUnit,BiocGenerics,knitr, curl, httr License: Artistic-2.0 MD5sum: cfc6d5a72878ec794ac0be88938cedfa NeedsCompilation: no Package: EnhancedVolcano Version: 1.2.0 Depends: ggplot2, ggrepel Suggests: RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, gridExtra, magrittr License: GPL-3 MD5sum: e07947292645c861e847cab9fcf60f84 NeedsCompilation: no Package: ENmix Version: 1.21.6 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats Imports: grDevices,graphics,preprocessCore,matrixStats,methods,utils, wateRmelon,sva,geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 1f4bc90f848a067c6c802c8be375151f NeedsCompilation: no Package: EnrichedHeatmap Version: 1.14.0 Depends: R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 1.99.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 354f237782eaf57e6c3ace742398e126 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.14.3 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap, DESeq2, EDASeq, GSEABase, GO.db, KEGGREST, KEGGgraph, MASS, ReportingTools, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma, methods, pathview, rappdirs, safe, topGO Suggests: ALL, BiocStyle, airway, hgu95av2.db, knitr License: Artistic-2.0 MD5sum: 6e8169ad80ef917ddea224de05360caa NeedsCompilation: no Package: enrichplot Version: 1.4.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, purrr, RColorBrewer, reshape2, stats, UpSetR, utils Suggests: clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc License: Artistic-2.0 MD5sum: 3842cd6f24eede4adb94dad3374f50a1 NeedsCompilation: no Package: enrichTF Version: 1.0.0 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats Suggests: knitr, magrittr, testthat License: GPL-3 MD5sum: 6d32698632dc4bd6b099d48325581b09 NeedsCompilation: no Package: ensembldb Version: 2.8.1 Depends: BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.29.10), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors, Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 657b222cbb206064bc80a63811c7476f NeedsCompilation: no Package: ensemblVEP Version: 1.26.1 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats Suggests: RUnit License: Artistic-2.0 MD5sum: ac30677a145ea068f906ffc7858d11a1 NeedsCompilation: no Package: ENVISIONQuery Version: 1.32.0 Depends: rJava, XML, utils License: GPL-2 MD5sum: 8e08095cda9c1a95d101e7568cf49d34 NeedsCompilation: no Package: EpiDISH Version: 2.0.2 Depends: R (>= 3.5) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 0924ada71c8694d640b3181de1bfc7e5 NeedsCompilation: no Package: epigenomix Version: 1.24.0 Depends: R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: 25ef016294642eea92f5861defac13f5 NeedsCompilation: no Package: epihet Version: 1.0.0 Depends: R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2, foreach, Rtsne, igraph Imports: data.table, doParallel, EntropyExplorer, graphics, stats, grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA Suggests: knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: c06c440713eb659c25de200098c28c1c NeedsCompilation: no Package: epiNEM Version: 1.8.0 Depends: R (>= 3.4) Imports: BoolNet, e1071, gtools, stats, igraph, nem, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db License: GPL-3 MD5sum: 76377c06686a8e5e8300c0c983923261 NeedsCompilation: no Package: epivizr Version: 2.14.0 Depends: R (>= 3.0), methods, Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle License: Artistic-2.0 MD5sum: e8327fa8707402547bf84be7693df002 NeedsCompilation: no Package: epivizrChart Version: 1.6.0 Depends: R (>= 3.4.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 67b9da7932bddf6246b6b86f84e153b1 NeedsCompilation: no Package: epivizrData Version: 1.12.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI License: MIT + file LICENSE MD5sum: 2f11801b5495e63deab2497ed1b92286 NeedsCompilation: no Package: epivizrServer Version: 1.12.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 1ebe50b859db578f50ff6068288efd38 NeedsCompilation: no Package: epivizrStandalone Version: 1.12.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: cab65c8a4b24d30beb55a608d6fbdc62 NeedsCompilation: no Package: erccdashboard Version: 1.18.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) MD5sum: 1032ec195ee26ce0239d120c955a83f9 NeedsCompilation: no Package: erma Version: 1.0.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors, BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: b42e8f00156c28d2698ba16c5585b758 NeedsCompilation: no Package: ERSSA Version: 1.2.0 Depends: R (>= 3.5.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 96c579e7c9d1351f8c6dc94e2c3bb38c NeedsCompilation: no Package: esATAC Version: 1.6.1 Depends: R (>= 3.5), Rsamtools, GenomicRanges, ShortRead Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, DiagrammeR, magrittr, digest, BSgenome, AnnotationDbi, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2016, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg, testthat, webshot License: GPL-3 | file LICENSE Archs: x64 MD5sum: ae20e0a977233e9604c01f0b1a634932 NeedsCompilation: yes Package: esetVis Version: 1.10.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment License: GPL-3 MD5sum: 0d9a30c4788017d0dd9aa162ce949901 NeedsCompilation: no Package: eudysbiome Version: 1.14.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 047a92ad163d17b14f550850e37eb0e7 NeedsCompilation: no Package: evaluomeR Version: 1.0.63 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment Imports: cluster (>= 2.0.7-1), corrplot (>= 0.84), grDevices, graphics, stats, Rdpack Suggests: BiocStyle, knitr, rmarkdown, kableExtra, magrittr License: GPL-3 MD5sum: 466f07edd430776fc4dabdf76e96d0c5 NeedsCompilation: no Package: EventPointer Version: 2.2.4 Depends: R (>= 3.4), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, BSgenome.Hsapiens.UCSC.hg38, Biostrings Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: afdedb4d78043df647149eab0cba0a3e NeedsCompilation: no Package: ExCluster Version: 1.2.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: 5028118a73918c8857db5fd7e96db56f NeedsCompilation: no Package: ExiMiR Version: 2.26.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 MD5sum: 4dd952a0c5f77f86265721357dc47d1f NeedsCompilation: no Package: exomeCopy Version: 1.30.0 Depends: IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools Imports: stats4, methods, GenomeInfoDb Suggests: Biostrings License: GPL (>= 2) MD5sum: e68955655de5d7df8b919f6b029b3be0 NeedsCompilation: yes Package: exomePeak Version: 2.17.0 Depends: R (>= 3.5.0), Rsamtools, GenomicFeatures (>= 1.14.5), rtracklayer, GenomicAlignments License: GPL-2 MD5sum: 3456fc99d03482a26b4cd24a3333f7eb NeedsCompilation: no Package: ExperimentHub Version: 1.10.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.15.9), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, curl, rappdirs Suggests: knitr, BiocStyle Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: de16efc050b3675e822fbd241b1068c3 NeedsCompilation: no Package: ExperimentHubData Version: 1.10.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.13.11) Imports: methods, ExperimentHub, BiocManager, DBI, BiocCheck, httr, curl, biocViews, graph Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: a7707d43fbbd0db88936ba6a99a53400 NeedsCompilation: no Package: explorase Version: 1.48.0 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 MD5sum: 21248c0c7488ee0bf6077ccb03290d0c NeedsCompilation: no Package: ExpressionAtlas Version: 1.12.0 Depends: R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2 Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: a14c5b3cbe7c1c11e6f7b12290762eae NeedsCompilation: no Package: ExpressionView Version: 1.36.0 Depends: caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, affy License: GPL (>= 2) MD5sum: 42823dd1a231c96c1c8484403e95b652 NeedsCompilation: yes Package: fabia Version: 2.30.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 6c36dc1231f55f6469d11f4b76a49acc NeedsCompilation: yes Package: factDesign Version: 1.60.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: 9db80d51dde4fe4debf4bcd1317e331d NeedsCompilation: no Package: FamAgg Version: 1.12.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE MD5sum: 7d73b990b471a5bbc9a5f4a52010fdc1 NeedsCompilation: no Package: farms Version: 1.36.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) MD5sum: e03fed5237d059cc504f8311600938e1 NeedsCompilation: no Package: fastLiquidAssociation Version: 1.20.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: 86c29b5cd8edd17a1844abbc2c40281d NeedsCompilation: no Package: FastqCleaner Version: 1.2.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, methods, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL (>= 2) MD5sum: 9fd90848cb095f8768c8aa22cf426ab4 NeedsCompilation: yes Package: fastseg Version: 1.30.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo License: LGPL (>= 2.0) MD5sum: 3f4f576809b0b9de45d4e8ef2947eea6 NeedsCompilation: yes Package: FCBF Version: 1.2.5 Depends: R (>= 3.6) Imports: ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment, stats, mclust Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager License: MIT + file LICENSE MD5sum: fcae93cd605231f44aa77ced0fe5a6ba NeedsCompilation: no Package: fCCAC Version: 1.10.0 Depends: R (>= 3.3.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 MD5sum: 6614471a57447b3ba938fb723cd9e661 NeedsCompilation: no Package: fCI Version: 1.14.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: d886adcdcb84a88b0c24d8f4ae4d910a NeedsCompilation: no Package: fdrame Version: 1.56.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 8bb3059973a217274a7d8dec8a1250a3 NeedsCompilation: yes Package: FELLA Version: 1.4.1 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 68f3fb1787cfe00e4c93ffd949f34eb7 NeedsCompilation: no Package: FEM Version: 3.12.0 Depends: AnnotationDbi,Matrix,marray,corrplot,igraph,impute,limma,org.Hs.eg.db,graph,BiocGenerics Imports: graph License: GPL (>= 2) MD5sum: 0dfe9b41772263030ef193759c90acc3 NeedsCompilation: no Package: ffpe Version: 1.28.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 05ad7dc16b2f849f392123a3a6a8b7d2 NeedsCompilation: no Package: FGNet Version: 3.18.0 Depends: R (>= 2.15) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png Suggests: RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, BiocManager License: GPL (>= 2) MD5sum: 86c490d5ddaab231d0dfdd862f6aed95 NeedsCompilation: no Package: fgsea Version: 1.10.1 Depends: R (>= 3.3), Rcpp Imports: data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery License: MIT + file LICENCE MD5sum: f6476e58baf36abbcb6142b4966a643d NeedsCompilation: yes Package: FindMyFriends Version: 1.14.0 Imports: methods, BiocGenerics, Biobase, tools, dplyr, IRanges, Biostrings, S4Vectors, kebabs, igraph, Matrix, digest, filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro, BiocParallel, utils, stats LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown, reutils License: GPL (>= 2) MD5sum: 8f41164987f56ae09297da848cc88b31 NeedsCompilation: yes Package: FISHalyseR Version: 1.18.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: be6da4b0fcd9884da0ee3d01c3dcdf37 NeedsCompilation: no Package: fishpond Version: 1.0.2 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm License: GPL-2 MD5sum: bf36308f378d7dc3c3a57ce05b97ae0d NeedsCompilation: no Package: FitHiC Version: 1.10.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 9ad2ef5671bfce808db7f9f61c64b93d NeedsCompilation: yes Package: flagme Version: 1.40.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 836cd0c2d6ef6d6f58af43228416412d NeedsCompilation: yes Package: flowAI Version: 1.14.0 Depends: R (>= 3.4) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny License: GPL (>= 2) MD5sum: c887df5730d374cb7db2a7ef93524fe8 NeedsCompilation: no Package: flowBeads Version: 1.22.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: aa74d00c38b7ea468cf450e3ab01001e NeedsCompilation: no Package: flowBin Version: 1.20.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: bb3ae805b33e7df21ecf640f8cd5874f NeedsCompilation: no Package: flowcatchR Version: 1.18.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 9c3d6e42f7c1073343ca5c0854422759 NeedsCompilation: no Package: flowCHIC Version: 1.18.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 MD5sum: 63c39e1f2a05a49e65601574812b1a21 NeedsCompilation: no Package: flowCL Version: 1.22.0 Depends: R (>= 3.4), Rgraphviz, SPARQL Imports: methods, grDevices, utils, graph Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 0144cde0951e98a4f7a8471693807a52 NeedsCompilation: no Package: flowClean Version: 1.22.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 MD5sum: 2b64b477a320b1858313596eb698a805 NeedsCompilation: no Package: flowClust Version: 3.22.0 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, ellipse, flowViz, flowCore, clue, corpcor, mnormt, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto License: Artistic-2.0 MD5sum: 53d5656c14e1ba05708c2492ec629315 NeedsCompilation: yes Package: flowCore Version: 1.50.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), graph, grDevices, graphics, methods, rrcov, stats, utils, stats4, corpcor, Rcpp, matrixStats, MASS LinkingTo: Rcpp, BH(>= 1.65.0.1) Suggests: Rgraphviz, flowViz, flowStats, testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 MD5sum: fd5fe2da3e045833d245472bfb1d92df NeedsCompilation: yes Package: flowCyBar Version: 1.20.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: 3a40a7203f7e9b7ea9fd8b14a61e30cc NeedsCompilation: no Package: flowDensity Version: 1.18.0 Imports: flowCore, graphics, car, sp, rgeos, gplots, RFOC, flowWorkspace (>= 3.20.5), methods, stats, grDevices License: Artistic-2.0 MD5sum: 8f3b83a8621c85305349c9e6e4a07e73 NeedsCompilation: no Package: flowFit Version: 1.22.0 Depends: R (>= 2.12.2) Imports: flowCore, flowViz, graphics, kza, methods, minpack.lm, gplots Suggests: flowFitExampleData License: Artistic-2.0 MD5sum: bebb60e166df9b96234595340d3ce45e NeedsCompilation: no Package: flowFP Version: 1.42.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 MD5sum: 42394f73038de936b2d9ad3b82bceee4 NeedsCompilation: yes Package: flowMap Version: 1.22.0 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), scales(>= 0.2.3), Matrix(>= 1.1-4), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 1956f3a204de01fecfbeb7ad53d2f824 NeedsCompilation: no Package: flowMatch Version: 1.20.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: a9f89f20a689dcf0acfb8f6f72fe47e8 NeedsCompilation: yes Package: flowMeans Version: 1.44.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: 26cf203fb97eed85439fc524aa63c39a NeedsCompilation: no Package: flowMerge Version: 2.32.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: aa5796d15c5bbe1e10f1d1204cafe657 NeedsCompilation: no Package: flowPeaks Version: 1.30.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 MD5sum: 8af65bebd3bc3545a27d8f0d9da6c741 NeedsCompilation: yes Package: flowPloidy Version: 1.10.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: 8e4270702378029e598d7b82be4177a4 NeedsCompilation: no Package: flowPlots Version: 1.32.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: 7006726f05d103ef51ab895d105c2b5e NeedsCompilation: no Package: flowQB Version: 2.11.1 Imports: methods, flowCore (>= 1.32.0), stats, extremevalues Suggests: flowQBData, FlowRepositoryR, xlsx, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 3326238deb71a39ac4cfa69c29dc76c1 NeedsCompilation: no Package: FlowRepositoryR Version: 1.16.0 Depends: R (>= 3.2) Imports: XML, RCurl, tools, utils, jsonlite Suggests: RUnit, BiocGenerics, flowCore, methods License: Artistic-2.0 MD5sum: 412477b926637675d6c9b2dbd0d07c1f NeedsCompilation: no Package: FlowSOM Version: 1.16.0 Depends: R (>= 3.2), igraph Imports: flowCore, ConsensusClusterPlus, BiocGenerics, tsne, XML, flowUtils Suggests: BiocStyle License: GPL (>= 2) MD5sum: b28182a7c8e7d0a062c93d7e709ab789 NeedsCompilation: yes Package: flowStats Version: 3.42.0 Depends: R (>= 2.10), flowCore, cluster, flowWorkspace, ncdfFlow(>= 2.19.5) Imports: BiocGenerics, MASS, flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice,ks, RColorBrewer Suggests: xtable, testthat Enhances: RBGL,graph License: Artistic-2.0 MD5sum: e79d22f2752f9f575bd057c3bed7fd5b NeedsCompilation: no Package: flowTime Version: 1.8.0 Depends: R (>= 3.4), flowCore, plyr Imports: utils Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats License: Artistic-2.0 MD5sum: d14bb00e157e0c1204f1304d9106b693 NeedsCompilation: no Package: flowTrans Version: 1.36.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 5be3fa82b2892bc99ad35307f9395b35 NeedsCompilation: no Package: flowType Version: 2.22.0 Depends: R (>= 2.10), Rcpp (>= 0.10.4), BH (>= 1.51.0-3) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats LinkingTo: Rcpp, BH Suggests: xtable License: Artistic-2.0 MD5sum: ee8256e879c82ce3ea542245b829c72a NeedsCompilation: yes Package: flowUtils Version: 1.48.0 Depends: R (>= 2.2.0) Imports: Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 MD5sum: 6e5a358c3a1fef2abfe65b50f0dbc32f NeedsCompilation: no Package: flowViz Version: 1.48.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats,knitr License: Artistic-2.0 MD5sum: 6919f8a0332621f4805e2b395c9c58b7 NeedsCompilation: no Package: flowVS Version: 1.16.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 MD5sum: b664e794b1e3998631475b893d92bc39 NeedsCompilation: no Package: flowWorkspace Version: 3.32.0 Depends: R (>= 2.16.0),flowCore(>= 1.49.10),ncdfFlow(>= 2.25.4) Imports: Biobase, BiocGenerics, graph, graphics, grDevices, lattice, methods, stats, stats4, utils, RBGL, tools, gridExtra, Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, scales, flowViz, matrixStats, digest, RcppParallel LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel Suggests: testthat, flowWorkspaceData, knitr, ggcyto, parallel, CytoML License: Artistic-2.0 MD5sum: 797fa4879c1d4bab3f8daf1a845eac98 NeedsCompilation: yes Package: fmcsR Version: 1.26.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: a4e4eb7851b2c51f6f21a85ac7af7247 NeedsCompilation: yes Package: focalCall Version: 1.18.0 Depends: R(>= 2.10.0), CGHcall Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: c555b50351bca8977b62353027cc35f1 NeedsCompilation: no Package: FoldGO Version: 1.2.3 Depends: R (>= 3.5) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: df4fabb59f2def7a932a0b2bfdfa31fc NeedsCompilation: no Package: FourCSeq Version: 1.18.0 Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11), splines, methods, LSD Imports: DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) MD5sum: 8433a631778a0686ed1107a965e96e8b NeedsCompilation: no Package: FRGEpistasis Version: 1.20.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 37952e856c57599225394728b3730b97 NeedsCompilation: no Package: frma Version: 1.36.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 94bf551993ea56f77e48330bfe13b0db NeedsCompilation: no Package: frmaTools Version: 1.36.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: db1ec01c20b52ddc34d3c8161bf13da4 NeedsCompilation: no Package: FunChIP Version: 1.10.0 Depends: R (>= 3.2), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 24e2ce91810cb2a528e349b51e968597 NeedsCompilation: yes Package: FunciSNP Version: 1.28.0 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1), ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Suggests: org.Hs.eg.db Enhances: parallel License: GPL-3 MD5sum: 62d1b1948e8ebd9737593809f8644870 NeedsCompilation: no Package: funtooNorm Version: 1.8.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: b6d50989a81ea88fe52f9bf110a7bd17 NeedsCompilation: no Package: GA4GHclient Version: 1.8.0 Depends: S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 8ef72497f8aed503e012fa063162a496 NeedsCompilation: no Package: GA4GHshiny Version: 1.6.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: a619b2ae29713b73728f89295c804fe0 NeedsCompilation: no Package: gaga Version: 2.30.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: fe0fd738660de0e168906463bee2143c NeedsCompilation: yes Package: gage Version: 2.34.0 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 986f20d5fa1a55d8f9a6f90e42ffbf73 NeedsCompilation: no Package: gaggle Version: 1.52.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: 4c1228a547ec5dd7bc84989fe799167c NeedsCompilation: no Package: gaia Version: 2.28.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 1f9c21a6827807196e692492a66421a4 NeedsCompilation: no Package: GAPGOM Version: 1.0.0 Depends: R (>= 3.6.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE MD5sum: f759c198b3ba235a97ca2aa9774957c6 NeedsCompilation: no Package: GAprediction Version: 1.10.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 90976d9f97e8ca28b0f6f54e07a142a5 NeedsCompilation: no Package: garfield Version: 1.12.0 Suggests: knitr License: GPL-3 MD5sum: 6716cb811197c02cd261b63f47272001 NeedsCompilation: yes Package: GARS Version: 1.4.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: b665e44406eda49f0709b6fd442b69ec NeedsCompilation: no Package: GateFinder Version: 1.4.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 761325ed0ae4c8fd95f7e6209b21a4ce NeedsCompilation: no Package: gcapc Version: 1.8.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: f607d7621f7ace1805fcd7a3afd84641 NeedsCompilation: no Package: gcatest Version: 1.14.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 443b739eb0572f57d9a0a6d7e4a2a620 NeedsCompilation: yes Package: gCMAP Version: 1.28.0 Depends: GSEABase, limma (>= 3.20.0) Imports: Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi, DESeq, grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras (>= 1.1.2) Suggests: BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa License: Artistic-2.0 OS_type: unix MD5sum: 059af72e07332cff9038a6abe84cf21a NeedsCompilation: no Package: gCMAPWeb Version: 1.24.0 Depends: Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook Imports: brew, BiocGenerics, annotate, AnnotationDbi, graphics, grDevices, GSEABase, hwriter, parallel, stats, utils, yaml Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit Enhances: bigmemory, bigmemoryExtras License: Artistic-2.0 OS_type: unix MD5sum: 271ff957589aeabcef3b64198399ad4d NeedsCompilation: no Package: gCrisprTools Version: 1.12.0 Depends: R (>= 3.3) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e5485064448e1a89aedae9dbb1725be1 NeedsCompilation: no Package: gcrma Version: 2.56.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 62510ade73f9c0b8823e51b6bff2c322 NeedsCompilation: yes Package: GDCRNATools Version: 1.4.1 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 889e2c261ce1a51910dbd3fee239f0b9 NeedsCompilation: no Package: GDSArray Version: 1.4.2 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: f5ff717369cb6c0267dc12c9d9eff387 NeedsCompilation: no Package: gdsfmt Version: 1.20.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, crayon, RUnit, knitr, BiocGenerics License: LGPL-3 MD5sum: 5778f3ca0a10bc914759350f8d42e091 NeedsCompilation: yes Package: geecc Version: 1.18.0 Depends: R (>= 3.3.0), methods Imports: MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils LinkingTo: Rcpp Suggests: hgu133plus2.db, GO.db, AnnotationDbi License: GPL (>= 2) MD5sum: 4f779900b8bc8e0953aa230712cc1f61 NeedsCompilation: yes Package: GEM Version: 1.10.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: 2e92486e419e74aa7da4884e857cb7ad NeedsCompilation: no Package: genArise Version: 1.60.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 402bb601fc9494da58dacac7c66457f6 NeedsCompilation: no Package: genbankr Version: 1.12.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 282798884cfbad30dc4ff75b1498c910 NeedsCompilation: no Package: GeneAccord Version: 1.2.0 Depends: R (>= 3.5) Imports: biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools, ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats, tibble, utils Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat License: file LICENSE MD5sum: 2af2f56aea9f6d6e079a19365ece474a NeedsCompilation: no Package: GeneAnswers Version: 2.26.0 Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate, downloader Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) MD5sum: fd8e5e90f98efbb2045e11d42e1b1f36 NeedsCompilation: no Package: geneAttribution Version: 1.10.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 37a9d2c93f2b96fd64ca5e27574680a0 NeedsCompilation: no Package: GeneBreak Version: 1.14.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: dc709035c22b79fe16ce899a4e300857 NeedsCompilation: no Package: geneClassifiers Version: 1.8.0 Depends: utils Imports: methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 70331d8e3d86ebc811c144dd58759ca4 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.30.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 295460a18d140851e6f3852e80973cd4 NeedsCompilation: no Package: genefilter Version: 1.66.0 Imports: S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 89a16c8a1c9ec26f6429981b785a15b0 NeedsCompilation: yes Package: genefu Version: 2.16.0 Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10) Imports: amap, impute Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival License: Artistic-2.0 MD5sum: 55607b25477679e847b5febd2b8345e0 NeedsCompilation: no Package: GeneGA Version: 1.34.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: e4fe3036db49cde6d708962fd1ed1739 NeedsCompilation: no Package: GeneGeneInteR Version: 1.10.0 Depends: R (>= 3.5) Imports: snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 31d000883a38923e0e8b964c92f73d40 NeedsCompilation: yes Package: GeneMeta Version: 1.56.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: edea7656bc37bd90cf806f5bffead15f NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.26.1 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb License: GPL (>= 2) MD5sum: 2368103d418be3c5f50cae8c80967cd1 NeedsCompilation: yes Package: GeneOverlap Version: 1.20.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: c16764bedae345b804a1178d788f2ce0 NeedsCompilation: no Package: geneplast Version: 1.10.3 Depends: R (>= 3.3), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr License: GPL (>= 2) MD5sum: 0d89206caa35c9c0d8f7f91cf98f15c4 NeedsCompilation: no Package: geneplotter Version: 1.62.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: f682017835f9a7eeffa925eaac8f71f9 NeedsCompilation: no Package: geneRecommender Version: 1.56.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 3d86561defb5cdd99161a27b05877bab NeedsCompilation: no Package: GeneRegionScan Version: 1.40.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 68b83d6f500c10572e4d015ba84ccb66 NeedsCompilation: no Package: geneRxCluster Version: 1.20.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8c38b2da8fef36460b58499de0326f98 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.28.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) MD5sum: d872e68b8285183d0d7ab04aa7233f22 NeedsCompilation: yes Package: GENESIS Version: 2.14.4 Imports: Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, dplyr, foreach, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, poibin, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: e988cd00e402a237243ef59ca2822d08 NeedsCompilation: no Package: GeneStructureTools Version: 1.4.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 05cb8f5f2ca9b74c09c5633ff75050d9 NeedsCompilation: no Package: geNetClassifier Version: 1.24.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 47c050a36340a35356171d886ccd9cf7 NeedsCompilation: no Package: GeneticsDesign Version: 1.52.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 MD5sum: 5219e9f8a29fe16b38de31f69c170236 NeedsCompilation: no Package: GeneticsPed Version: 1.46.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: bbe9e968038a3b327d34e53292cdbbd5 NeedsCompilation: yes Package: geneXtendeR Version: 1.10.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: 450c027fe6c2ae4934dd24a8686e2236 NeedsCompilation: yes Package: GENIE3 Version: 1.6.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 535e4bf9a25c52f26feb09ac5e790016 NeedsCompilation: yes Package: genoCN Version: 1.36.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 90b9be077f52a563e6d3a046c3c8a6af NeedsCompilation: yes Package: GenoGAM Version: 2.2.0 Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>= 1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.9.34), Matrix (>= 1.2-8), data.table (>= 1.9.4) Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>= 1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17), DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods, stats LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown License: GPL-2 MD5sum: 10eeda50dcae803a3fc0cffcce6eefad NeedsCompilation: yes Package: genomation Version: 1.16.0 Depends: R (>= 3.0.0),grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: a7ad497efb9e2fda03c6c37ce19eed8c NeedsCompilation: yes Package: GenomeGraphs Version: 1.44.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 MD5sum: 67809498b9dfae83aabac0bf220eb35f NeedsCompilation: no Package: GenomeInfoDb Version: 1.20.0 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: cecf189c70fce6130d357c0a8c46eb01 NeedsCompilation: no Package: genomeIntervals Version: 1.40.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 43bb686102c90ce961b0b6351e0e3589 NeedsCompilation: no Package: genomes Version: 3.14.0 Depends: readr, curl License: GPL-3 MD5sum: a077a69631cbe6acd0cd2e691c7cae06 NeedsCompilation: no Package: GenomicAlignments Version: 1.20.1 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.19.11), IRanges (>= 2.15.12), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.33.4), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: dd8feb48156b562146ea74b699432d1b NeedsCompilation: yes Package: GenomicDataCommons Version: 1.8.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 MD5sum: 7a1b67231b1ccc299aa857334cc6b8fb NeedsCompilation: no Package: GenomicFeatures Version: 1.36.4 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.15.4), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 863880059ab7513c986cea6c5eea669d NeedsCompilation: no Package: GenomicFiles Version: 1.20.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 315822cd8b9c8a8be88deb9aebf37e56 NeedsCompilation: no Package: GenomicInteractions Version: 1.18.1 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, BiocStyle, testthat License: GPL-3 MD5sum: a582ed2c731656a2f55ded7184fbfd08 NeedsCompilation: no Package: GenomicRanges Version: 1.36.1 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.19.11), IRanges (>= 2.17.1), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.19.8) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle License: Artistic-2.0 MD5sum: 6ad9a0c74dacf0a7f78e539efab42c5d NeedsCompilation: yes Package: GenomicScores Version: 1.8.1 Depends: R (>= 3.4), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings, BSgenome, GenomeInfoDb, AnnotationHub Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer License: Artistic-2.0 MD5sum: 38d1e0f6d4972ea49776b64b4973c22b NeedsCompilation: no Package: GenomicTuples Version: 1.18.1 Depends: R (>= 3.3.0), GenomicRanges (>= 1.31.8), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.13.13), data.table, stats4 LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 55133b45b2e8ff1ed86481fc6c096ea8 NeedsCompilation: yes Package: Genominator Version: 1.38.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 MD5sum: 3d84c0c525066a75bba4249dc5676d07 NeedsCompilation: no Package: genoset Version: 1.40.0 Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>= 1.17.19), SummarizedExperiment (>= 1.1.6) Imports: S4Vectors (>= 0.13.13), GenomeInfoDb (>= 1.1.3), IRanges (>= 2.5.12), methods, graphics Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 MD5sum: 9c639a14b97c90b50581c7c44fa2575e NeedsCompilation: yes Package: genotypeeval Version: 1.16.0 Depends: R (>= 3.4.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 5f5c8d95fb9dd6fa0487c43c400d5515 NeedsCompilation: no Package: genphen Version: 1.12.1 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) MD5sum: e813d03f944c4ea715e7087475544530 NeedsCompilation: no Package: GenRank Version: 1.12.0 Depends: R (>= 3.2.3) Imports: matrixStats, reshape2, survcomp Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: dad9e212df456a6ccd2c25ca658ec132 NeedsCompilation: no Package: GenVisR Version: 1.16.1 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis, data.table, BSgenome, grDevices, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: 461a60bd88a957c24daddcb9892a41e7 NeedsCompilation: no Package: GEOmetadb Version: 1.46.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: f6d5d27fe6addf6f4daf72b82372b8ad NeedsCompilation: no Package: GEOquery Version: 2.52.0 Depends: methods, Biobase Imports: httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr License: GPL-2 MD5sum: ab0f2d2a69f1cbd845ab7cbe225c3ba9 NeedsCompilation: no Package: GEOsubmission Version: 1.36.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 4bc67c34e3a62253a1b0e79e6cc915e7 NeedsCompilation: no Package: gep2pep Version: 1.4.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: d4bdd65369f474f7b3d17ac060fc0347 NeedsCompilation: no Package: gespeR Version: 1.16.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: d2b3ea34d9d1c043f889a02fb111451b NeedsCompilation: no Package: GEWIST Version: 1.28.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: eed2a055a18ee166af153d06ca0410ee NeedsCompilation: no Package: GGBase Version: 3.46.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db, knitr License: Artistic-2.0 MD5sum: 40c2bc7b7cb9bfdb3fca63e092e29888 NeedsCompilation: no Package: ggbio Version: 1.32.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 5ee3dd6b46d554ca569c2b9dc71e429d NeedsCompilation: no Package: ggcyto Version: 1.12.0 Depends: methods, ggplot2(>= 2.2.1.9000), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.17.24) Imports: plyr, scales, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: Artistic-2.0 MD5sum: 4c9443a3bbee4ff09ef9b8e413b40328 NeedsCompilation: no Package: GGtools Version: 5.20.0 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 MD5sum: b54d30694006d2f291c7b717a39c56d3 NeedsCompilation: no Package: ggtree Version: 1.16.6 Depends: R (>= 3.4.0) Imports: ape, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck (>= 0.1.0), tidyr, tidytree (>= 0.2.4), treeio (>= 1.7.3), utils Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, scales, testthat, tibble License: Artistic-2.0 MD5sum: f61a268e7b8858c6774b57e9b290d700 NeedsCompilation: no Package: GIGSEA Version: 1.2.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 722ecfa98d287f8380af786f160492f9 NeedsCompilation: no Package: girafe Version: 1.36.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: da9585bea6624a78478137c4ccb901c1 NeedsCompilation: yes Package: GISPA Version: 1.8.0 Depends: R (>= 3.3.2) Imports: Biobase, changepoint, data.table, genefilter, graphics, GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats Suggests: knitr License: GPL-2 MD5sum: 375f9485d8ba68a0267fa3d38fcaba0f NeedsCompilation: no Package: GLAD Version: 2.48.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 3f5b35a21a75186227d262647b59f35b NeedsCompilation: yes Package: GladiaTOX Version: 1.0.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: bd7ad2050bd0e42d250712d6d72be21f NeedsCompilation: no Package: Glimma Version: 1.12.0 Depends: R (>= 3.4.0) Imports: edgeR, grDevices, jsonlite, methods, stats, S4Vectors, utils Suggests: BiocStyle, IRanges, GenomicRanges, SummarizedExperiment, DESeq2, limma, testthat, knitr, rmarkdown, pryr License: GPL-3 | file LICENSE MD5sum: 8fe9db52a5ebc432f8cab7071d33a14d NeedsCompilation: no Package: glmSparseNet Version: 1.2.0 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2, survminer, reshape2, stats, stringr, rlang, parallel, methods, loose.rock (>= 1.0.12) Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL (>= 3) MD5sum: 817ed7ae4523b36a77614b93c9bdf173 NeedsCompilation: no Package: GlobalAncova Version: 4.2.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 24e42662d9e3fd5eea193bad02300c8f NeedsCompilation: yes Package: globalSeq Version: 1.12.0 Depends: R (>= 3.5.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 0052e28fb11a8c9575baa1a55b4a3b74 NeedsCompilation: no Package: globaltest Version: 5.38.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: a93ffe229a13c2b8ae1e0bfab3ae7088 NeedsCompilation: no Package: gmapR Version: 1.26.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: f7730c3b5581e3ce7b4ef1b3093ba1ee NeedsCompilation: yes Package: GMRP Version: 1.12.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: e11678c64a96380d6c9e45e55d4625a8 NeedsCompilation: no Package: GNET2 Version: 1.0.0 Depends: R (>= 3.5) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 2bf1f758fca46085479a0bde5375fc15 NeedsCompilation: yes Package: GOexpress Version: 1.18.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: 629c508e879921a4a5e8e8a77f8d0bd6 NeedsCompilation: no Package: GOfuncR Version: 1.4.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 74726fe990476fa6b666cf2b5bb9eba4 NeedsCompilation: yes Package: GOFunction Version: 1.32.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0), Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>= 1.10.2), SparseM (>= 0.85) Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI, SparseM License: GPL (>= 2) MD5sum: 2c06746ecbd128cf9b3015f1b02562e7 NeedsCompilation: no Package: GOpro Version: 1.10.0 Depends: R (>= 3.4) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 32d15cff75940d97854d32a844fa5fdb NeedsCompilation: yes Package: goProfiles Version: 1.46.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: fd64c57600d8c94f0e32f8dd51e0f2f3 NeedsCompilation: no Package: GOSemSim Version: 2.10.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat License: Artistic-2.0 MD5sum: 7c3863de574a9827b66b3fec462ae4d8 NeedsCompilation: yes Package: goseq Version: 1.36.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 4d129450dfb15d6d4c0dfaad38049082 NeedsCompilation: no Package: GOSim Version: 1.22.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) MD5sum: a40a2a17bb04a80fa603731be6cc7874 NeedsCompilation: yes Package: goSTAG Version: 1.8.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 9cc1c101e786c4d899963065072348c0 NeedsCompilation: no Package: GOstats Version: 2.50.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 18ba9b92fb8f33ed241d15ea0a6c8b06 NeedsCompilation: no Package: GOsummaries Version: 2.20.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) MD5sum: 58fda5df6b523c4d578e9fdc3ae05ee1 NeedsCompilation: yes Package: GOTHiC Version: 1.20.6 Depends: R (>= 3.5.0), methods, utils, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager Suggests: HiCDataLymphoblast, parallel License: GPL-3 MD5sum: d330a36156c60c46f952b1b63aa69a52 NeedsCompilation: no Package: goTools Version: 1.58.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: e2d72bfb02d9979dfeef7e6bc5d17c65 NeedsCompilation: no Package: gpart Version: 1.2.0 Depends: R (>= 3.5.0), grid, Homo.sapiens, TxDb.Hsapiens.UCSC.hg38.knownGene, Imports: igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi, grDevices, stats, utils, GenomicRanges, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 1331072984139386a31e1218ad5d5203 NeedsCompilation: yes Package: gpls Version: 1.56.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 13093d7b8ea0811da3ff37cb5f332ac3 NeedsCompilation: no Package: gprege Version: 1.28.0 Depends: R (>= 2.10), gptk Suggests: spam License: AGPL-3 MD5sum: 9c0b44c318ff09818ff49a50e0fee651 NeedsCompilation: no Package: gQTLBase Version: 1.16.0 Imports: GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors, BiocGenerics, foreach, doParallel, bit, ff, rtracklayer, ffbase, GenomicFiles, SummarizedExperiment Suggests: geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack License: Artistic-2.0 MD5sum: 73e850aa5a1ff008660ac575a99e8006 NeedsCompilation: no Package: gQTLstats Version: 1.16.0 Depends: R (>= 3.1.0), Homo.sapiens Imports: methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges, SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs, gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures, ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc, beeswarm, HardyWeinberg, graphics, stats, utils, shiny, plotly, erma, ggbeeswarm Suggests: geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio, BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock License: Artistic-2.0 MD5sum: ebda0ef678142318e1aa07668efea57f NeedsCompilation: no Package: graper Version: 1.0.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 3cf8669879141e500e5f69ec7004637b NeedsCompilation: yes Package: graph Version: 1.62.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 MD5sum: 5b665791d49e3e87757e6f0cf1c27acf NeedsCompilation: yes Package: GraphAlignment Version: 1.48.0 License: file LICENSE License_restricts_use: yes MD5sum: 7001972152fb1cd966f873d62f6100ff NeedsCompilation: yes Package: GraphAT Version: 1.56.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 1cb0ccafa1dc19eda5c0dd9c628df925 NeedsCompilation: no Package: graphite Version: 1.30.0 Depends: R (>= 2.10), methods Imports: AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils Suggests: a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 559dbd9b8368b238afaa3784083fb4dc NeedsCompilation: no Package: GraphPAC Version: 1.26.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 9b4dbec7c57284685df2391f3d95e8c0 NeedsCompilation: no Package: GRENITS Version: 1.36.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 92261713a716c49379d2ee4b6e2c6308 NeedsCompilation: yes Package: GreyListChIP Version: 1.16.0 Depends: R (>= 3.5), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit Enhances: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: c0294f8e0ec2b37ace8520022cc71000 NeedsCompilation: no Package: GRmetrics Version: 1.10.0 Depends: R (>= 3.3), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 30fe04b3ef445896e2551fcc7ba75eaa NeedsCompilation: no Package: groHMM Version: 1.18.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 8983dcbac6cd3cf84433640e07ea4207 NeedsCompilation: yes Package: GRridge Version: 1.8.0 Depends: R (>= 3.2), penalized, Iso, survival, methods, graph,stats,glmnet,mvtnorm Suggests: testthat License: GPL-3 MD5sum: 15d439eaf17d228970bce90e32c35825 NeedsCompilation: no Package: GSALightning Version: 1.12.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 88df9d921afbca1265815c27f4f4532b NeedsCompilation: no Package: GSAR Version: 1.18.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: f53c56d21969b346b9ddd9da63bb45c0 NeedsCompilation: no Package: GSCA Version: 2.14.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 8ff07dab7380213bff28935f8f9d362b NeedsCompilation: no Package: GSEABase Version: 1.46.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 6e562d9bbdc3e1305b0af55f106e418f NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.4.0 Depends: Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, GEOquery, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, rappdirs, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6666b019e68213e8fb990d28955ade35 NeedsCompilation: no Package: GSEAlm Version: 1.44.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 44954c57f7ebdd5e32d0a86d2961a28c NeedsCompilation: no Package: gsean Version: 1.4.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA License: Artistic-2.0 MD5sum: f6381b7ee7c8d515568c970921768f54 NeedsCompilation: no Package: GSReg Version: 1.18.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 75a7727c6c3ec5dddbd7fe272c65b2d1 NeedsCompilation: yes Package: GSRI Version: 2.32.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: fb44aa45a4375a0e2b7b6ed0c4604285 NeedsCompilation: no Package: GSVA Version: 1.32.0 Depends: R (>= 3.0.0) Imports: methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4), geneplotter, shiny, shinythemes Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, snow, parallel, GSVAdata License: GPL (>= 2) MD5sum: fbf37c12f2e4ddbefffe06d68a49c54c NeedsCompilation: yes Package: gtrellis Version: 1.16.1 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: ce8f4a61af353c18f6858ad26a7af639 NeedsCompilation: no Package: GUIDEseq Version: 1.14.0 Depends: R (>= 3.2.0), GenomicRanges, BiocGenerics Imports: BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: 1f6c785e409fd430fd39babe82a8b53d NeedsCompilation: no Package: Guitar Version: 2.0.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 6d39650e6b2647c97fdb54ff80fa1357 NeedsCompilation: no Package: Gviz Version: 1.28.3 Depends: R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8) Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra, rmarkdown, testthat License: Artistic-2.0 MD5sum: 2b6922894ac535c6049ad915e979b585 NeedsCompilation: no Package: gwascat Version: 2.16.1 Depends: R (>= 3.5.0), Homo.sapiens Imports: methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, Biostrings, Rsamtools, rtracklayer, AnnotationDbi Suggests: DO.db, DT, utils, knitr, RBGL, RUnit, snpStats, Gviz, VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio, ggplot2, DelayedArray Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: b1f457e35c45954b8d8f4cfc2daf5898 NeedsCompilation: no Package: GWASTools Version: 1.30.1 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation License: Artistic-2.0 MD5sum: 959b43880c9eec928aa181ca80f7fe62 NeedsCompilation: no Package: gwasurvivr Version: 1.2.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 4903756809691e97955b79d0f185aa1f NeedsCompilation: no Package: h5vc Version: 2.18.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 1.99.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.15.3) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 7e2c123b13cf7d854810bb8e47c93e8a NeedsCompilation: yes Package: hapFabia Version: 1.26.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: a63686618465f59c0545d0b36c51f238 NeedsCompilation: yes Package: Harman Version: 1.12.0 Depends: R (>= 3.5) Imports: Rcpp (>= 0.11.2), graphics, stats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 52cf3b3f74e74865d98703cb842681aa NeedsCompilation: yes Package: Harshlight Version: 1.56.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: fd903a7f83459d6bf07f5ee37b2b606e NeedsCompilation: yes Package: HCABrowser Version: 1.0.1 Depends: R (>= 3.6.0), dplyr Imports: BiocFileCache, S4Vectors, googleAuthR, httr, jsonlite, methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 2816b383b5a286f19b2c116ccd41d2b8 NeedsCompilation: no Package: HDF5Array Version: 1.12.3 Depends: R (>= 3.4), methods, DelayedArray (>= 0.9.3), rhdf5 (>= 2.25.6) Imports: utils, tools, BiocGenerics (>= 0.25.1), S4Vectors, IRanges LinkingTo: S4Vectors (>= 0.21.6), Rhdf5lib Suggests: h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle License: Artistic-2.0 MD5sum: 5781ae54e339cbf0921b29b64b4f8ac8 NeedsCompilation: yes Package: HDTD Version: 1.18.0 Depends: R (>= 3.4) Imports: stats, Rcpp (>= 0.12.13) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, markdown License: GPL-3 MD5sum: 96e4ebd46143fc76f1a8fd2f91978c14 NeedsCompilation: yes Package: heatmaps Version: 1.8.0 Depends: R (>= 3.4) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 3f929be2441b272387c5a7e59289cc47 NeedsCompilation: no Package: Heatplus Version: 2.30.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: f2b40b768decb8a280ab1d5bb4212d14 NeedsCompilation: no Package: HelloRanges Version: 1.10.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle License: GPL (>= 2) MD5sum: 2162f8502e0051913184575fbed4ac7b NeedsCompilation: no Package: HELP Version: 1.42.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: 779de524a7e41ec6fcdc7fe2f45e252b NeedsCompilation: no Package: HEM Version: 1.56.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: 8ac3fc2efa22e3d98e544b79834d337d NeedsCompilation: yes Package: hiAnnotator Version: 1.18.0 Depends: GenomicRanges, R (>= 2.10) Imports: foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2, scales, methods Suggests: knitr, doParallel, testthat, BiocGenerics License: GPL (>= 2) MD5sum: 5e82f0d2242854d2462903c158f78b0c NeedsCompilation: no Package: HIBAG Version: 1.20.0 Depends: R (>= 3.2.0) Imports: methods Suggests: parallel, knitr, gdsfmt (>= 1.2.2), SNPRelate (>= 1.1.6), ggplot2, reshape2 License: GPL-3 MD5sum: 726af2e377f5adb21cbceeadfc75e7d4 NeedsCompilation: yes Package: HiCBricks Version: 1.2.0 Depends: R (>= 3.5), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3b982b5180601d94f1d5d0dfb4e96665 NeedsCompilation: no Package: HiCcompare Version: 1.6.0 Depends: R (>= 3.4.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: 89f5a317b6381160c2ef31d6b2d8c553 NeedsCompilation: no Package: hicrep Version: 1.8.0 Depends: R (>= 3.4) Imports: stats Suggests: knitr, rmarkdown, testthat License: GPL (>= 2.0) MD5sum: 8eb8f8a4541cfd57b3dbdb43e83dafac NeedsCompilation: no Package: hierGWAS Version: 1.14.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: 517560970b191c05a63c080c2abe8956 NeedsCompilation: no Package: hierinf Version: 1.2.0 Depends: R (>= 3.5.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: 4c22ae972ff46a7b71014120383c3cf9 NeedsCompilation: no Package: HilbertCurve Version: 1.14.0 Depends: R (>= 3.1.2), grid Imports: methods, utils, HilbertVis, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong License: MIT + file LICENSE MD5sum: 0f13456bc1c6c31c6d12556d7a4d756f NeedsCompilation: no Package: HilbertVis Version: 1.42.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: b944cceadff5086688b47e2b5141b7dc NeedsCompilation: yes Package: HilbertVisGUI Version: 1.42.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) MD5sum: 267f2b6f362c492e5452fc3ee14e2ee4 NeedsCompilation: yes Package: hipathia Version: 2.0.0 Depends: R (>= 3.5), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: f7a13083f09722dba0d15cfea6fc3c8f NeedsCompilation: no Package: hiReadsProcessor Version: 1.20.1 Depends: Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R (>= 3.0) Imports: sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods Suggests: knitr, testthat License: GPL-3 MD5sum: b4a03ff6f6b0a2a2f88958dee8b1775e NeedsCompilation: no Package: HIREewas Version: 1.2.1 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: 0fe0588c64d86ecfdca40da8d1e4134a NeedsCompilation: yes Package: HiTC Version: 1.28.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, GenomeInfoDb Suggests: BiocStyle, HiCDataHumanIMR90 License: Artistic-2.0 MD5sum: 80af3724d38ab86abf8f7e0eb0fb1649 NeedsCompilation: no Package: hmdbQuery Version: 1.4.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat License: Artistic-2.0 MD5sum: 07e6442e9fa2d86e879df03d9472b6fe NeedsCompilation: no Package: HMMcopy Version: 1.26.0 Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0) License: GPL-3 MD5sum: e18ef3f2af6b9d913c127002b9ca729b NeedsCompilation: yes Package: hopach Version: 2.44.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: a38ccfbd7bd30f6258d05248aea93788 NeedsCompilation: yes Package: HPAanalyze Version: 1.2.1 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, readr, tibble, xml2, tidyr, stats, utils, hpar, gridExtra Suggests: knitr, rmarkdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 6aa86b4a8d20f43ee34299a921ad326c NeedsCompilation: no Package: hpar Version: 1.26.0 Depends: R (>= 2.15) Imports: utils Suggests: org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat License: Artistic-2.0 MD5sum: c4c17d1b40dd4a13e17a570ebae93480 NeedsCompilation: no Package: HTqPCR Version: 1.38.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: cbef56085d20388836c255a4db656852 NeedsCompilation: no Package: HTSanalyzeR Version: 2.36.0 Depends: R (>= 2.15), igraph, methods Imports: graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 MD5sum: b9f2093f422cb35e3f3fe2f4730ae15f NeedsCompilation: no Package: HTSeqGenie Version: 4.14.0 Depends: R (>= 3.0.0), gmapR (>= 1.8.0), ShortRead (>= 1.19.13), VariantAnnotation (>= 1.8.3) Imports: BiocGenerics (>= 0.2.0), S4Vectors (>= 0.9.25), IRanges (>= 1.21.39), GenomicRanges (>= 1.23.21), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0), Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel, parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments, VariantTools (>= 1.7.7), GenomeInfoDb, SummarizedExperiment, methods Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db License: Artistic-2.0 MD5sum: d46082df22d3f967a24751a34d62a293 NeedsCompilation: no Package: htSeqTools Version: 1.31.0 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, S4Vectors, IRanges, methods, MASS, BSgenome, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.11) Enhances: parallel,multicore License: GPL (>= 2) MD5sum: 67c17cf06f81100c8d00c6e62abb7a56 NeedsCompilation: no Package: HTSFilter Version: 1.24.0 Depends: R (>= 3.4) Imports: edgeR (>= 3.9.14), DESeq2 (>= 1.10.1), DESeq (>= 1.22.1), BiocParallel (>= 1.4.3), Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq (>= 2.1.4), BiocStyle, testthat License: Artistic-2.0 MD5sum: 81e0bf6630e03003acf58479e7a2dff1 NeedsCompilation: no Package: HumanTranscriptomeCompendium Version: 1.0.1 Depends: R (>= 3.6) Imports: shiny, ssrch, S4Vectors, SummarizedExperiment, utils Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, BiocManager License: Artistic-2.0 MD5sum: d8eebe5373f787346a241b27c036c48b NeedsCompilation: no Package: HybridMTest Version: 1.28.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: 2adb9c6540ab27cedb4faa03e4583ac9 NeedsCompilation: no Package: hypeR Version: 1.00.0 Depends: R (>= 3.6.0) Imports: plotly, DT, magrittr, dplyr, openxlsx, msigdbr, Suggests: devtools, testthat, knitr, httr License: GPL-3 + file LICENSE MD5sum: 4f570fff06ca8963acdc11a0b8a3650b NeedsCompilation: no Package: hyperdraw Version: 1.36.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: bee18ff39dabc8070d4158ab8744d35e NeedsCompilation: no Package: hypergraph Version: 1.56.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 1be01b3c5187c8683d98db1d2562b3eb NeedsCompilation: no Package: iASeq Version: 1.28.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: c075e378b12b5200ad884c08a9350651 NeedsCompilation: no Package: iasva Version: 1.2.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 MD5sum: 35ce6227d603e3cd72c02473af7e8a5b NeedsCompilation: no Package: iBBiG Version: 1.28.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: a8c422a7147d66279038caa3afbd353b NeedsCompilation: yes Package: ibh Version: 1.32.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: d647de7adf78295460f5242db08080d6 NeedsCompilation: no Package: iBMQ Version: 1.24.0 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 MD5sum: d578e07476692cef041d52c6e55c7a94 NeedsCompilation: yes Package: iCARE Version: 1.12.0 Depends: R (>= 3.3.0), plotrix, gtools, Hmisc Suggests: RUnit, BiocGenerics License: GPL-3 + file LICENSE MD5sum: c919f4b68a344684f824fee6cc3cf899 NeedsCompilation: yes Package: Icens Version: 1.56.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: 5678e335cfd93285441e49987a9c6896 NeedsCompilation: no Package: icetea Version: 1.2.0 Depends: R (>= 3.5) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 0e9cc78eaa1af347642bf79736f01f42 NeedsCompilation: no Package: iCheck Version: 1.14.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: 11e302f09eccac2f8ac6a5c774c9df7d NeedsCompilation: no Package: iChip Version: 1.38.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: c9a7577c9aa5e5deeb81cc7d75c92158 NeedsCompilation: yes Package: iClusterPlus Version: 1.20.0 Depends: R (>= 3.3.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: eaa03f67d33b21acc645d6da575e8cbc NeedsCompilation: yes Package: iCNV Version: 1.4.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 6bcbd715cf66112e385017113c0053ce NeedsCompilation: no Package: iCOBRA Version: 1.12.1 Depends: R (>= 3.4) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 2.0.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 828a059e483805bce96828c45cf6e86e NeedsCompilation: no Package: ideal Version: 1.8.1 Depends: topGO Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), d3heatmap, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE MD5sum: 9ab37f2bfe0b80136510b9fd0e818ae4 NeedsCompilation: no Package: IdeoViz Version: 1.20.0 Depends: Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer,graphics,GenomeInfoDb License: GPL-2 MD5sum: 34b57513cb86906e68de69fa85af6904 NeedsCompilation: no Package: idiogram Version: 1.60.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 2de17d1e45f463dc6fb1d54fde8b8520 NeedsCompilation: no Package: IdMappingAnalysis Version: 1.28.0 Depends: R (>= 2.14), R.oo (>= 1.13.0), rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 MD5sum: 86f495894ba88140d217d1a26c492171 NeedsCompilation: no Package: IdMappingRetrieval Version: 1.32.0 Depends: R.oo, XML, RCurl, rChoiceDialogs Imports: biomaRt, ENVISIONQuery, AffyCompatible, R.methodsS3, utils License: GPL-2 MD5sum: 227712f71934cd713feb497ceacb2849 NeedsCompilation: no Package: iGC Version: 1.14.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: ec8a4c87e5d4db0f99530f45062fc34f NeedsCompilation: no Package: igvR Version: 1.4.0 Depends: R (>= 3.5.0), GenomicRanges, VariantAnnotation, GenomicAlignments, rtracklayer, BrowserViz (>= 2.5.14) Imports: methods, BiocGenerics, httpuv, utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 40f1f3d7da5dd3bde91bcf550d964bec NeedsCompilation: no Package: IHW Version: 1.12.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 6a4b581a105d27072db9cb26a332de6e NeedsCompilation: no Package: illuminaio Version: 0.26.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: bfcf25ce8fe6d149909e61885527b966 NeedsCompilation: yes Package: imageHTS Version: 1.34.0 Depends: R (>= 2.9.0), EBImage (>= 4.3.12), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 Suggests: BiocStyle, MASS License: LGPL-2.1 MD5sum: a2a6b427bd861f6f0e13b46f3c6bd6d3 NeedsCompilation: no Package: IMAS Version: 1.8.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats, ggfortify, grDevices, methods, Matrix, utils, graphics, gridExtra, grid, lattice, Rsamtools, survival, BiocParallel, GenomicAlignments, parallel Suggests: BiocStyle, RUnit License: GPL-2 MD5sum: 2bbe62f67811961074d499b7927f7465 NeedsCompilation: no Package: Imetagene Version: 1.14.0 Depends: R (>= 3.2.0), metagene, shiny Imports: d3heatmap, shinyBS, shinyFiles, shinythemes, ggplot2 Suggests: knitr, BiocStyle, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 079bec706473caf6d5b36a0ecadbf963 NeedsCompilation: no Package: IMMAN Version: 1.4.0 Imports: STRINGdb, Biostrings, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 0d83a0ca90c511709dc5f03f97a07d49 NeedsCompilation: no Package: ImmuneSpaceR Version: 1.12.2 Imports: utils, R6, data.table, curl, httr, Rlabkey (>= 2.1.136), Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots, plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown, preprocessCore, flowCore, flowWorkspace, digest Suggests: knitr, testthat License: GPL-2 MD5sum: 2157e52581a662aeef30ba491ed7cb96 NeedsCompilation: no Package: immunoClust Version: 1.16.0 Depends: R(>= 3.3), methods, stats, graphics, grid, lattice, grDevices, flowCore Suggests: BiocStyle License: Artistic-2.0 MD5sum: 75cb645cc6c100e4899d21444fa92c85 NeedsCompilation: yes Package: IMPCdata Version: 1.20.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: 10a82494a1fc776a715f32bf010d6fcb NeedsCompilation: no Package: ImpulseDE Version: 1.10.0 Depends: graphics, grDevices, stats, utils, parallel, compiler, R (>= 3.2.3) Imports: amap, boot Suggests: longitudinal, knitr License: GPL-3 MD5sum: d3fc8f7a9a204922e9b52a91bb2ae113 NeedsCompilation: no Package: ImpulseDE2 Version: 1.8.0 Imports: Biobase, BiocParallel, ComplexHeatmap, circlize, compiler, cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods, S4Vectors, stats, SummarizedExperiment, utils License: Artistic-2.0 MD5sum: d5c0703064c18d87df62b888b81d2569 NeedsCompilation: no Package: impute Version: 1.58.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: a2cd42f981e6f84c3d8dd43589cdf8ec NeedsCompilation: yes Package: INDEED Version: 1.2.0 Depends: R (>= 3.5), glasso (>= 1.8) Imports: utils (>= 3.3.1), stats (>= 3.3.1), graphics (>= 3.3.1), devtools (>= 1.13.0) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: 2dfab78fbd3675f6b52145078dd60c03 NeedsCompilation: no Package: infercnv Version: 1.0.4 Depends: R(>= 3.6) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, Matrix, fastcluster, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, reshape, rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 6252b31304118fe382f15ffed3e942b6 NeedsCompilation: no Package: InPAS Version: 1.16.3 Depends: R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr License: GPL (>= 2) MD5sum: f3a582128b32c2b70d5e093e6efe79a6 NeedsCompilation: no Package: INPower Version: 1.20.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: f2956f51c54c958ef26f6e5fb5514053 NeedsCompilation: no Package: INSPEcT Version: 1.14.0 Depends: R (>= 3.2), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, compiler, preprocessCore, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, DESeq2, plgem, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr License: GPL-2 MD5sum: b7c4434d8f6346e3b3751eb8a7bd50f7 NeedsCompilation: no Package: InTAD Version: 1.4.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 629fffc8ce328eb60cfa3c52cc9b2907 NeedsCompilation: no Package: intansv Version: 1.24.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: Artistic-2.0 MD5sum: 9e7fea98fb594a592249a9c8d7aadb8f NeedsCompilation: no Package: InteractionSet Version: 1.12.0 Depends: GenomicRanges, SummarizedExperiment Imports: IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 07e6970639ef0dbd8a73837560b37d61 NeedsCompilation: yes Package: interactiveDisplay Version: 1.22.0 Depends: R (>= 2.10), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: 9f41ae1b1f2663388f320e616e6f1c86 NeedsCompilation: no Package: interactiveDisplayBase Version: 1.22.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny Suggests: knitr Enhances: rstudioapi License: Artistic-2.0 MD5sum: 69e4cf7831b72ac47f40df36c2db1ddb NeedsCompilation: no Package: IntEREst Version: 1.8.0 Depends: R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors Imports: seqLogo, Biostrings, GenomicFeatures, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 9b3f4c58a0efe17843478e5bc800486e NeedsCompilation: no Package: InterMineR Version: 1.6.1 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db License: LGPL MD5sum: e705e0148a268717c461a2c188c1fd93 NeedsCompilation: no Package: IntramiRExploreR Version: 1.6.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 2afcd5b9e14a10fef5cf8f4c9cfcbd3f NeedsCompilation: no Package: inveRsion Version: 1.32.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) MD5sum: 8baae537f75d3a562e69b34a66def929 NeedsCompilation: yes Package: IONiseR Version: 2.8.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 59bcb7f086b55f1551a88c2fb0542535 NeedsCompilation: no Package: iPAC Version: 1.28.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 MD5sum: 1fdc1f29676fbb941f029d10b87044d2 NeedsCompilation: no Package: ipdDb Version: 1.2.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: d9255c8440a60b0dff66aaf02291e498 NeedsCompilation: no Package: IPO Version: 1.10.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils Imports: BiocParallel Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr Enhances: parallel License: GPL (>= 2) + file LICENSE MD5sum: dc27b55b709bae8e44e74d442792bcd8 NeedsCompilation: no Package: IPPD Version: 1.32.0 Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops Imports: methods, stats, graphics License: GPL (>= 2) MD5sum: 8945de40830ddf1cf423a7ebacd346e7 NeedsCompilation: yes Package: IRanges Version: 2.18.3 Depends: R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.21.9) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 0ebb6d162b170bb07aafe794014fef37 NeedsCompilation: yes Package: iSEE Version: 1.4.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, colourpicker, igraph, vipor, mgcv, reshape2, rentrez, AnnotationDbi, graphics, grDevices, viridisLite, cowplot, scales, dplyr Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools License: MIT + file LICENSE MD5sum: 09c890984d49ca15e67da9c23b40bc28 NeedsCompilation: no Package: iSeq Version: 1.36.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 34fcf377d00fe05b4fb3fd030c73f960 NeedsCompilation: yes Package: isobar Version: 1.30.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: b7ee8950caf1433708ff8ac6b95260d9 NeedsCompilation: no Package: IsoCorrectoR Version: 1.2.1 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a59a913c2c0af39cbdb3a126e15c7bf2 NeedsCompilation: no Package: IsoCorrectoRGUI Version: 1.0.2 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6b3b23893b98ae3f38e724ad10d6d91b NeedsCompilation: no Package: IsoformSwitchAnalyzeR Version: 1.6.0 Depends: R (>= 3.5), limma, DEXSeq, ggplot2 Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), edgeR, futile.logger, stringr, dplyr, magrittr, readr, XVector Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund License: GPL (>= 2) MD5sum: 7dd5e98185805f3db37b5721a227a9bb NeedsCompilation: yes Package: IsoGeneGUI Version: 2.20.0 Depends: tcltk, xlsx Imports: Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer, Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg Suggests: RUnit License: GPL-2 MD5sum: a14a8953f9c3cc6c45c5d22d0a9c0345 NeedsCompilation: no Package: ISoLDE Version: 1.12.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: 276c0974c5b41c30d6838ecb3a9c4432 NeedsCompilation: yes Package: isomiRs Version: 1.12.0 Depends: R (>= 3.5), DiscriMiner, SummarizedExperiment Imports: AnnotationDbi, assertive.sets, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: b4aed94aabd853358bfee3e7110766ab NeedsCompilation: no Package: ITALICS Version: 2.44.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: e6f57ef7c5bbe5ed02dd9cb61250f250 NeedsCompilation: no Package: iterativeBMA Version: 1.42.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: c26210dc91288d115df41cc61354a7d4 NeedsCompilation: no Package: iterativeBMAsurv Version: 1.42.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: aaa6fc21790a7635efadeed3a38844dc NeedsCompilation: no Package: iterClust Version: 1.6.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE MD5sum: 70ac9c78685bb43b679b7ff045973b48 NeedsCompilation: no Package: iteremoval Version: 1.4.0 Depends: R (>= 3.5.0), ggplot2 (>= 2.2.1) Imports: magrittr, graphics, utils, GenomicRanges, SummarizedExperiment Suggests: testthat, knitr License: GPL-2 MD5sum: c46186d3425702960b2a52b9abf95e7d NeedsCompilation: no Package: IVAS Version: 2.4.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: f47596c3dd0e30e36ffd95202598ffb5 NeedsCompilation: no Package: ivygapSE Version: 1.6.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat License: Artistic-2.0 MD5sum: d65a1bbbb18590ab5d4511c32db0b219 NeedsCompilation: no Package: IWTomics Version: 1.8.0 Depends: GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: 83f139dee1677f2058729a33253ff7af NeedsCompilation: no Package: joda Version: 1.32.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) MD5sum: dd636d646cd32887e7482c3d33790873 NeedsCompilation: no Package: JunctionSeq Version: 1.14.0 Depends: R (>= 3.2.2), methods, SummarizedExperiment (>= 0.2.0), Rcpp (>= 0.11.0), RcppArmadillo (>= 0.3.4.4) Imports: DESeq2 (>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase (>= 2.30.0), locfit, BiocGenerics (>= 0.7.5), BiocParallel, genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges, LinkingTo: Rcpp, RcppArmadillo Suggests: MASS, knitr, JctSeqData, BiocStyle Enhances: Cairo, pryr License: file LICENSE MD5sum: c86ceab0a76520077f0faaadeb246c90 NeedsCompilation: yes Package: karyoploteR Version: 1.10.5 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: ca8fe09a4a4dda893e83f58b6afa7674 NeedsCompilation: no Package: KCsmart Version: 2.42.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: 35a417f9b9b31b4564cc1e471d4e5755 NeedsCompilation: no Package: kebabs Version: 1.18.0 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3), S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 1ae029f6e3b610712443e5782250d37f NeedsCompilation: yes Package: KEGGgraph Version: 1.44.0 Depends: R (>= 2.10.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl Suggests: Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: e298c4cd0727be85b994ce6d55b231b1 NeedsCompilation: no Package: KEGGlincs Version: 1.10.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 36bea9619be4db9dcb06b96fd1e3412e NeedsCompilation: no Package: keggorthology Version: 2.36.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: a469c9ebfc6aa734e7ff0a370a76ea76 NeedsCompilation: no Package: KEGGprofile Version: 1.26.0 Depends: RCurl Imports: AnnotationDbi,png,TeachingDemos,XML,KEGG.db,KEGGREST,biomaRt License: GPL (>= 2) MD5sum: 91deb781c85b4721d458507ead2a49d4 NeedsCompilation: no Package: KEGGREST Version: 1.24.1 Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr License: Artistic-2.0 MD5sum: a9e8e0cc436e24919cb35d110ee71ad5 NeedsCompilation: no Package: kimod Version: 1.12.0 Depends: R(>= 3.3),methods Imports: cluster, graphics, Biobase License: GPL (>= 2) MD5sum: f5352633a9d77335245869357ea08738 NeedsCompilation: no Package: KinSwingR Version: 1.2.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b0df202538b540f80dfc3ce1df2d5efa NeedsCompilation: no Package: kissDE Version: 1.4.0 Imports: aod, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel Suggests: BiocStyle, testthat License: GPL (>= 2) MD5sum: 46b4f2ecba916fb54ee06357be23a29c NeedsCompilation: no Package: lapmix Version: 1.50.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) MD5sum: c651cdd30ef812c669b2b06561292126 NeedsCompilation: no Package: LBE Version: 1.52.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 MD5sum: b202a9fa83581c2ced9eda1b4878cedb NeedsCompilation: no Package: ldblock Version: 1.14.3 Depends: R (>= 3.1), methods, Homo.sapiens Imports: Matrix, snpStats, VariantAnnotation, GenomeInfoDb, Rsamtools, GO.db, GenomicFiles (>= 1.13.6), BiocGenerics (>= 0.25.1), EnsDb.Hsapiens.v75, ensembldb, httr Suggests: RUnit, BiocGenerics, knitr, gQTLstats License: Artistic-2.0 MD5sum: e22a14c861b4075c296cc025a390100b NeedsCompilation: no Package: LEA Version: 2.6.0 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: a20d7c2992d2218b872b637768cd24a1 NeedsCompilation: yes Package: LedPred Version: 1.18.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: a8c110446d86b622593f1326c4757d3c NeedsCompilation: no Package: les Version: 1.34.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 674dc44527723d71cfeccb035f328b1b NeedsCompilation: no Package: levi Version: 1.2.0 Depends: R(>= 3.5.0) Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 0540fd445269f0f76b769c52390cad03 NeedsCompilation: yes Package: lfa Version: 1.14.0 Depends: R (>= 3.2) Imports: corpcor Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 8ffc04644ae46e129d8f9c28094b67c1 NeedsCompilation: yes Package: limma Version: 3.40.6 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>= 2) MD5sum: 4ebb7afaf1095d9b5ac235f18e008095 NeedsCompilation: yes Package: limmaGUI Version: 1.60.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: da7cbfa9ead2ea122e7c1a4e4f048933 NeedsCompilation: no Package: LINC Version: 1.12.0 Depends: R (>= 3.3.1), methods, stats Imports: Rcpp (>= 0.11.0), DOSE, ggtree, gridExtra, ape, grid, png, Biobase, sva, reshape2, utils, grDevices, org.Hs.eg.db, clusterProfiler, ggplot2, ReactomePA LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, knitr, biomaRt License: Artistic-2.0 MD5sum: 5b3d4f07c51e87efa8b1894f69cfd085 NeedsCompilation: yes Package: LineagePulse Version: 1.4.0 Imports: BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils License: Artistic-2.0 MD5sum: 4284019bc000d29688f6141de4a5c344 NeedsCompilation: no Package: Linnorm Version: 2.8.0 Depends: R(>= 3.4) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat License: MIT + file LICENSE MD5sum: f7a2a4de6993c6351ae07f7d70370deb NeedsCompilation: yes Package: lipidr Version: 1.0.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, covr, spelling License: MIT + file LICENSE MD5sum: a827e4309c6d3751f78e194bd2b4668d NeedsCompilation: no Package: LiquidAssociation Version: 1.38.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 8ff9e0913456b720c8366e01ec419d48 NeedsCompilation: no Package: lmdme Version: 1.26.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 546f6d67cd946e4d9d81632e2214ee41 NeedsCompilation: no Package: LMGene Version: 2.40.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL MD5sum: 0073afa14740274f430c190c90ae3f2b NeedsCompilation: no Package: LOBSTAHS Version: 1.10.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 4153540588b21a7939bcd124d4b01ed7 NeedsCompilation: no Package: loci2path Version: 1.4.0 Depends: R (>= 3.4) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: a887d9af75e7ab94335dd7335f3048f2 NeedsCompilation: no Package: logicFS Version: 2.4.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: a63b247f856912abb2fe160c3d3b7039 NeedsCompilation: no Package: logitT Version: 1.42.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) MD5sum: 26d824e6c1b564e3e6ad3d86f8765124 NeedsCompilation: yes Package: Logolas Version: 1.8.0 Depends: R (>= 3.4) Imports: grid, SQUAREM, LaplacesDemon, stats, graphics, utils, ggplot2, gridBase, Biostrings Suggests: knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo License: GPL (>= 2) MD5sum: 72af8e4603d85cfe4c8c2e63bcdface6 NeedsCompilation: no Package: lol Version: 1.32.0 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 MD5sum: 5454962e90b5ded1b75a52788f8ddb31 NeedsCompilation: no Package: LOLA Version: 1.14.0 Depends: R (>= 2.10) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: c058753a3f86f5cecef272313d90f6b1 NeedsCompilation: no Package: LoomExperiment Version: 1.2.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, rtracklayer Imports: DelayedArray, GenomicRanges, HDF5Array, stats, utils Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: a06d4541c1ab40fc8dd322308a3ea0d7 NeedsCompilation: no Package: LowMACA Version: 1.14.1 Depends: R (>= 2.10) Imports: cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer, methods, LowMACAAnnotation, BiocParallel, motifStack, Biostrings, httr, grid, gridBase Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d1f3df0c3f461321cdc4474afd23df3b NeedsCompilation: no Package: LPE Version: 1.58.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: 1771e59d10976d6bc23c35a5b919c8fb NeedsCompilation: no Package: LPEadj Version: 1.44.0 Depends: LPE Imports: LPE, stats License: LGPL MD5sum: 399c100e5653af8e3a44a40690d85961 NeedsCompilation: no Package: lpNet Version: 2.16.0 Depends: lpSolve, nem License: Artistic License 2.0 MD5sum: 3c07b7d48480cc94e895140d38ac0767 NeedsCompilation: no Package: lpsymphony Version: 1.12.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr Enhances: slam License: EPL MD5sum: acce764137f7f9a82443decd693b5efb NeedsCompilation: yes Package: LRBaseDbi Version: 1.2.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 MD5sum: 6ea76caccdee3afc0765ace6a3ee6370 NeedsCompilation: no Package: lumi Version: 2.36.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: cb0925407710d86cc84f39ff5f971fe9 NeedsCompilation: no Package: LVSmiRNA Version: 1.34.0 Depends: R (>= 3.1.0), methods, splines Imports: BiocGenerics, stats4, graphics, stats, utils, MASS, Biobase, quantreg, limma, affy, SparseM, vsn, zlibbioc Enhances: parallel,snow, Rmpi License: GPL-2 MD5sum: 6e6961cde4bccf6e492cfe3283c2b490 NeedsCompilation: yes Package: LymphoSeq Version: 1.12.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 8f0f2ee5a5a72794136a79e4ee8ecc98 NeedsCompilation: no Package: M3C Version: 1.6.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc, dendextend, sigclust, Rtsne, survival, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: f23daab52c79f49bafba10a97f6bed97 NeedsCompilation: no Package: M3D Version: 1.18.0 Depends: R (>= 3.3.0) Imports: parallel, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: Artistic License 2.0 MD5sum: 68024daf277220047ac158ce60b1f461 NeedsCompilation: yes Package: M3Drop Version: 1.10.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase License: GPL (>= 2) MD5sum: 9683152b6e21fa7f3078e84619bff56b NeedsCompilation: no Package: maanova Version: 1.54.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) MD5sum: 5e95bee8b96e44435ec6d3d482ee2ceb NeedsCompilation: yes Package: macat Version: 1.58.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 MD5sum: f6f33205bbc943513b0ad8bcfcf1acfb NeedsCompilation: no Package: maCorrPlot Version: 1.54.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: e7a012e07292b0a09b4ab3b781d7e609 NeedsCompilation: no Package: MACPET Version: 1.4.0 Depends: R (>= 3.6), InteractionSet (>= 1.11.2), bigmemory (>= 4.5.33), BH (>= 1.66.0.1), Rcpp (>= 1.0.1) Imports: intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools (>= 1.99.4), stats (>= 3.6.0), utils (>= 3.6.0), methods (>= 3.6.0), GenomicRanges (>= 1.35.1), S4Vectors (>= 0.21.21), IRanges (>= 2.17.4), GenomeInfoDb (>= 1.19.2), gtools (>= 3.8.1), GenomicAlignments (>= 1.19.1), knitr (>= 1.22), rtracklayer (>= 1.43.3), BiocParallel (>= 1.17.18), Rbowtie (>= 1.23.3), GEOquery (>= 2.51.5), Biostrings (>= 2.51.5), ShortRead (>= 1.41.0), futile.logger (>= 1.4.3) LinkingTo: Rcpp, bigmemory, BH Suggests: ggplot2 (>= 3.1.0), igraph (>= 1.2.4), rmarkdown (>= 1.12), reshape2 (>= 1.4.3), BiocStyle (>= 2.11.0) License: GPL-3 MD5sum: 194312a63083aaf1fe4333ecab11fd12 NeedsCompilation: yes Package: made4 Version: 1.58.0 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 MD5sum: 00c2a89c91fb59c1ee485cd754d8f538 NeedsCompilation: no Package: MADSEQ Version: 1.10.0 Depends: R(>= 3.4), rjags(>= 4-6), Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: 7e62d154cf3cf3b0e18dd3987918ff47 NeedsCompilation: no Package: maftools Version: 2.0.16 Depends: R (>= 3.3) Imports: data.table, cometExactTest, RColorBrewer, NMF, methods, wordcloud, grDevices, survival Suggests: knitr, rmarkdown, BSgenome, Biostrings, mclust, rjson License: MIT + file LICENSE MD5sum: 5311469e8f6c7d824afe1335e6bc40e4 NeedsCompilation: no Package: MAGeCKFlute Version: 1.4.3 Depends: R (>= 3.5), ggplot2, stats, grDevices, utils, gridExtra Imports: ggExtra, ggsci, ggrepel, clusterProfiler, png, data.table, pheatmap, sva, DOSE, biomaRt, grid, pathview Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db License: GPL (>= 3) MD5sum: 61424ecd0cdcedda31133e48287bebd8 NeedsCompilation: no Package: maigesPack Version: 1.48.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) MD5sum: bd7b7b4a8952913853d1f25c342f671b NeedsCompilation: yes Package: MAIT Version: 1.18.0 Depends: R (>= 2.10), CAMERA, Rcpp, pls Imports: gplots,e1071,class,MASS,plsgenomics,agricolae,xcms,methods,caret Suggests: faahKO Enhances: rgl License: GPL-2 MD5sum: ebad68909a67b2224649a8ec8583d38c NeedsCompilation: no Package: makecdfenv Version: 1.60.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: 79ef6ba4960a32d7691d7428a58aa89b NeedsCompilation: yes Package: MANOR Version: 1.56.0 Depends: R (>= 2.10), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 MD5sum: fa54da1038acb0b053315892539d8dd0 NeedsCompilation: yes Package: manta Version: 1.30.0 Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13) Imports: Hmisc, caroline(>= 0.6.6) Suggests: RSQLite, plotrix License: Artistic-2.0 MD5sum: 0ceb88d84dff7742d4dcc6cc53e5ef2c NeedsCompilation: no Package: MantelCorr Version: 1.54.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: dd59c2cb7112102a25e153f10432ea6e NeedsCompilation: no Package: mAPKL Version: 1.14.1 Depends: R (>= 3.6.0), Biobase Imports: multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi, methods, parmigene,igraph,reactome.db Suggests: BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 116da278be7af23529028a147363ce80 NeedsCompilation: no Package: maPredictDSC Version: 1.22.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: 2d5cd443eb8639b69b8421686a834a79 NeedsCompilation: no Package: mapscape Version: 1.8.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c9408c2837e9ddeacfcf9f676b4589d4 NeedsCompilation: no Package: marray Version: 1.62.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: d2628eb19ca37a181402798dc8543ec9 NeedsCompilation: no Package: martini Version: 1.4.0 Depends: R (>= 3.5) Imports: igraph (>= 1.0.1), Matrix, methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), S4Vectors (>= 0.12.2), stats, utils LinkingTo: Rgin, Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), httr (>= 1.2.1), IRanges (>= 2.8.2), knitr, testthat, tidyverse, rmarkdown License: MIT + file LICENSE MD5sum: 55b0a9fc5a85e9499c83db57640c0472 NeedsCompilation: yes Package: maser Version: 1.2.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE MD5sum: faf35d96da67a1559eb6c9eb65b34280 NeedsCompilation: no Package: maSigPro Version: 1.56.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: 0b3ed0e8fd063fbf6700d64d2300082a NeedsCompilation: no Package: maskBAD Version: 1.28.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: 908a121329b4d59a384fb44921547c5c NeedsCompilation: no Package: MassArray Version: 1.36.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 9bcb895ad4c9c4e7100d65de88baf906 NeedsCompilation: no Package: massiR Version: 1.20.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: f5a3d0d1e7f63a5da7bd5dc4d7bfbbdd NeedsCompilation: no Package: MassSpecWavelet Version: 1.50.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) MD5sum: 6715f272814bb903e02be64a15d18a0c NeedsCompilation: yes Package: MAST Version: 1.10.0 Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, blme, SummarizedExperiment(>= 1.5.3), progress Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), roxygen2(> 4.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater License: GPL (>= 2) MD5sum: 6095a6cedbe585761fbb1c8df4ce9ea6 NeedsCompilation: no Package: matchBox Version: 1.26.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: cb3a8fdbf40e1dc8d26533bb1fd6a7f8 NeedsCompilation: no Package: MatrixRider Version: 1.16.0 Depends: R (>= 3.1.2) Imports: methods, TFBSTools, IRanges, XVector, Biostrings LinkingTo: IRanges, XVector, Biostrings, S4Vectors Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 License: GPL-3 MD5sum: 7f85bfa32fc6a25b3b6987e8a3f064fa NeedsCompilation: yes Package: matter Version: 1.10.0 Depends: R (>= 3.5), BiocParallel, methods, stats, biglm Imports: BiocGenerics, digest, irlba, utils Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 80c2d4693acc88b40867e100e4ade2dd NeedsCompilation: yes Package: MaxContrastProjection Version: 1.8.0 Depends: R (>= 3.4) Imports: EBImage, stats, methods Suggests: knitr, BiocStyle, testthat License: Artistic-2.0 MD5sum: a4636912f434c1ec7ecfe24743e77a06 NeedsCompilation: no Package: MBAmethyl Version: 1.18.0 Depends: R (>= 2.15) License: Artistic-2.0 MD5sum: 46b488829917ef5750391463877be1ab NeedsCompilation: no Package: MBASED Version: 1.18.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 992a08870864f79fa226791b969c3b8b NeedsCompilation: no Package: MBCB Version: 1.38.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) MD5sum: fa2a4736e30c0df5d78602349fda7852 NeedsCompilation: no Package: mbkmeans Version: 1.0.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, knitr, testthat License: MIT + file LICENSE MD5sum: d48afe30bbd4b7fc336a4e3021442e73 NeedsCompilation: yes Package: mBPCR Version: 1.38.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) MD5sum: c7a90c7e1527258452c9793cb06532ab NeedsCompilation: no Package: MBttest Version: 1.12.0 Depends: R (>= 3.3.0), stats, gplots, gtools,graphics,base, utils,grDevices Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: d65acd60c9194c071d70909738d8363c NeedsCompilation: no Package: mcaGUI Version: 1.32.0 Depends: lattice, MASS, proto, foreign, gWidgets(>= 0.0-36), gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca Enhances: iplots, reshape, ggplot2, cairoDevice, OTUbase License: GPL (>= 2) MD5sum: 1b55ca169ec63abfd1a4ca454cbbd8a7 NeedsCompilation: no Package: MCbiclust Version: 1.8.0 Depends: R (>= 3.4) Imports: BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 MD5sum: 48e7603efa86b31fff7a2a9d50cf5b78 NeedsCompilation: no Package: MCRestimate Version: 2.40.0 Depends: R (>= 2.7.2), golubEsets (>= 1.4.6) Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics, grDevices, stats, utils Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) License: GPL (>= 2) MD5sum: a76acf3b63978eb5a1cf9c99540c5d19 NeedsCompilation: no Package: mCSEA Version: 1.4.0 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 MD5sum: 7a9cabd1953c0e519ee9efe5fa6476d0 NeedsCompilation: no Package: mdgsa Version: 1.16.0 Depends: R (>= 2.14) Imports: AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix Suggests: BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit, BiocGenerics License: GPL MD5sum: d2c1c33f82b90c3c12dfa048b879d6aa NeedsCompilation: no Package: mdp Version: 1.4.0 Depends: R (>= 3.5) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea License: GPL-3 MD5sum: 251498b10ed231066befda17a853a5b9 NeedsCompilation: no Package: mdqc Version: 1.46.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: 79dff4086686e27cc40bec33c13475b2 NeedsCompilation: no Package: MDTS Version: 1.4.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 MD5sum: 0e8eb9fb588b9952a92ce0dd081b70fc NeedsCompilation: no Package: MEAL Version: 1.14.0 Depends: R (>= 3.2.0), Biobase, MultiDataSet Imports: GenomicRanges, limma, DMRcate, vegan, BiocGenerics, minfi, IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute, Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA, graphics, stats, utils, matrixStats Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata License: Artistic-2.0 MD5sum: f1d54fb22bf6fe39a3fbc7674e7d6372 NeedsCompilation: no Package: MeasurementError.cor Version: 1.56.0 License: LGPL MD5sum: 5a2fbc85ddce4e114407282ba1289d7a NeedsCompilation: no Package: MEDIPS Version: 1.36.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) MD5sum: 91aa3cc0532aa4d5778c256eea57e8de NeedsCompilation: no Package: MEDME Version: 1.44.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) MD5sum: 62985b7b4ebe51262d25380963c26d4a NeedsCompilation: yes Package: MEIGOR Version: 1.18.0 Depends: Rsolnp, snowfall, CNORode, deSolve Suggests: CellNOptR License: GPL-3 MD5sum: 7f8232f8bc699168903b7f124bd890eb NeedsCompilation: no Package: Melissa Version: 1.0.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, clues, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 1c43fd1e2d6fd481079f43eac08c5483 NeedsCompilation: no Package: MergeMaid Version: 2.56.0 Depends: R (>= 2.10.0), survival, Biobase, MASS, methods License: GPL (>= 2) MD5sum: 85560308a14870e7e571a1a517830836 NeedsCompilation: no Package: Mergeomics Version: 1.12.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: b199d231ce140214caac7667f3142dad NeedsCompilation: no Package: MeSHDbi Version: 1.20.0 Depends: R (>= 3.0.1), BiocGenerics (>= 0.15.10) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: RUnit License: Artistic-2.0 MD5sum: 8e5ddfc622ed4f0ea2380222996695f1 NeedsCompilation: no Package: meshes Version: 1.10.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, GOSemSim (>= 1.99.3), MeSH.db, methods, rvcheck, utils Suggests: knitr, MeSH.Cel.eg.db, MeSH.Hsa.eg.db, prettydoc License: Artistic-2.0 MD5sum: fee72009cb9fd04feef89fe26f569dc7 NeedsCompilation: no Package: meshr Version: 1.20.0 Depends: R (>= 3.0.1) Imports: methods, stats, utils, fdrtool, MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSHDbi, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db, cummeRbund, org.Hs.eg.db, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 MD5sum: 14b9bd13f8dedc691b578adc0be88b04 NeedsCompilation: no Package: messina Version: 1.20.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: bfd3714601dfff75a4dd9be6c8a7a5d4 NeedsCompilation: yes Package: metaArray Version: 1.62.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 MD5sum: 083da57aabf27d356e0de1b8cbab1320 NeedsCompilation: yes Package: Metab Version: 1.18.0 Depends: xcms, R (>= 3.0.1), svDialogs Imports: pander Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 72560743a678a57eb3a634be599a72fd NeedsCompilation: no Package: metabomxtr Version: 1.18.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 9d9d01919c3c1a6862df51f84037f152 NeedsCompilation: no Package: MetaboSignal Version: 1.14.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 0871a575a25e669e1419961747e5ad3f NeedsCompilation: no Package: metaCCA Version: 1.12.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 02cd0b7e8ba5bf167a3313dd8397e03b NeedsCompilation: no Package: MetaCyto Version: 1.6.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr License: GPL (>= 2) MD5sum: 38315a7bc63f03a7f2fdf63a04671134 NeedsCompilation: no Package: metagene Version: 2.16.0 Depends: R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown, similaRpeak License: Artistic-2.0 | file LICENSE MD5sum: dad27037a0cf662f0db8b1ebbe83f3c8 NeedsCompilation: no Package: metagene2 Version: 1.0.0 Depends: R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, DBChIP, purrr, data.table, methods, dplyr, magrittr Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 381dbccb0c6a7b747e5261115f1970cd NeedsCompilation: no Package: metagenomeFeatures Version: 2.4.0 Depends: R (>= 3.5), Biobase (>= 2.17.8) Imports: Biostrings (>= 2.36.4), S4Vectors (>= 0.14.7), dplyr (>= 0.7.0), dbplyr(>= 1.0.0), stringr (>= 1.0.0), lazyeval (>= 0.1.10), RSQLite (>= 1.0.0), magrittr (>= 1.5), methods (>= 3.3.1), lattice (>= 0.20.33), ape (>= 3.5), DECIPHER (>= 2.4.0) Suggests: knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), devtools (>= 1.13.5), ggtree(>= 1.8.2), BiocStyle (>= 2.8.2), phyloseq (>= 1.24.2), forcats (>= 0.3.0), ggplot2 (>= 3.0.0) License: Artistic-2.0 MD5sum: 1c3987396555e229b181613b022514d2 NeedsCompilation: no Package: metagenomeSeq Version: 1.26.3 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench, IHW Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay License: Artistic-2.0 MD5sum: dfd231fbe3ace1bac860c452c27d94d8 NeedsCompilation: no Package: metahdep Version: 1.42.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 53978153bca3e1c0eeb53c335c52ece8 NeedsCompilation: yes Package: metaMS Version: 1.20.0 Depends: R (>= 2.10), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: d8fe444714c4b37bd55b105fb733dbe6 NeedsCompilation: no Package: MetaNeighbor Version: 1.4.0 Depends: R(>= 3.5) Imports: beanplot (>= 1.2), GenomicRanges (>= 1.34.0), gplots (>= 3.0.1), Matrix (>= 1.2), matrixStats (>= 0.54), Rcpp, RColorBrewer (>= 1.1), stats (>= 3.4), SummarizedExperiment (>= 1.12), utils (>= 3.4) LinkingTo: Rcpp Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: a56fc917c62d35882e3cda1aa7132759 NeedsCompilation: yes Package: metaSeq Version: 1.24.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 9849976f5f3130155bcc317d002c50a6 NeedsCompilation: no Package: metaseqR Version: 1.24.0 Depends: R (>= 2.13.0), EDASeq, DESeq, limma, qvalue Imports: edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite Enhances: parallel, TCC, RMySQL License: GPL (>= 3) MD5sum: c6754c642aa149667090c8b30c96d915 NeedsCompilation: no Package: metavizr Version: 1.8.0 Depends: R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table, Biobase, digest Imports: epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan, GenomeInfoDb, phyloseq, httr Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData License: MIT + file LICENSE MD5sum: 454f7b0bed4f0f936f91f8f92e6f8340 NeedsCompilation: no Package: MetCirc Version: 1.14.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), graphics (>= 3.5), grDevices (>= 3.5), methods (>= 3.5), scales (>= 0.3.0), shiny (>= 1.0.0), stats (>= 3.5) Suggests: BiocGenerics, knitr (>= 1.11) License: GPL-2 MD5sum: e4bdd5d5bf79760717004e0e768dc6fd NeedsCompilation: no Package: methimpute Version: 1.6.0 Depends: R (>= 3.4.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 8c2fce21cbc830cae5b9d64526c6b569 NeedsCompilation: yes Package: methInheritSim Version: 1.6.0 Depends: R (>= 3.4) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: 33436a108f37f5e549a03e6612dc89d0 NeedsCompilation: no Package: MethPed Version: 1.12.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 772eab7137db1e2a13f07fefcb3f0366 NeedsCompilation: no Package: MethTargetedNGS Version: 1.16.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: 560df7085ab23e24f4cbd039a2c5a7c3 NeedsCompilation: no Package: methVisual Version: 1.36.0 Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn, grid,sqldf Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges, stats, utils License: GPL (>= 2) MD5sum: 4b4766fc35ffaa8929472d59000dd7d1 NeedsCompilation: no Package: methyAnalysis Version: 1.26.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb, GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db Imports: grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 8a5dd849c1286e568fe64cbe9ffbf339 NeedsCompilation: no Package: MethylAid Version: 1.18.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: e9f8c4e6f49241bfb5ff9f0464ff6470 NeedsCompilation: no Package: methylGSA Version: 1.2.3 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 0f7f04dc677a201d594d186ae97cb762 NeedsCompilation: no Package: methylInheritance Version: 1.8.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: 37d08eb046e151e8acc867eaab557275 NeedsCompilation: no Package: methylKit Version: 1.10.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat,knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: a06456112ec7e30a1429d877edf44d32 NeedsCompilation: yes Package: MethylMix Version: 2.14.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 9a3202f240fc625c7f68f8659cba3382 NeedsCompilation: no Package: methylMnM Version: 1.22.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: c6e10d64eef549b55d4447db0264f60d NeedsCompilation: yes Package: methylPipe Version: 1.18.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: e671d3ee89cf1a770cf8ac13b919c284 NeedsCompilation: yes Package: MethylSeekR Version: 1.24.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 0dcc61e0699c68e56893d16c2d2230ff NeedsCompilation: no Package: methylumi Version: 2.30.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: e5e8dd104dba330867bb8b3c3a78922a NeedsCompilation: no Package: methyvim Version: 1.6.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData License: file LICENSE MD5sum: 8a62c97ee32462f27dec7a8b7f868b73 NeedsCompilation: no Package: MetID Version: 1.2.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 706e4dfefc5c60903c0248a9aeaf4272 NeedsCompilation: no Package: MetNet Version: 1.2.0 Depends: R (>= 3.5), stats (>= 3.5) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), methods (>= 3.5), mpmi (>= 0.42), parmigene (>= 1.0.2), ppcor (>= 1.1), rfPermute (>= 2.1.5), sna (>= 2.4), stabs (>= 0.6), WGCNA (>= 1.61) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), igraph (>= 1.1.2), knitr (>= 1.11) License: GPL-2 MD5sum: d3e06137d7f3e5d6aaca1891002998cb NeedsCompilation: no Package: mfa Version: 1.6.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 314a4a4488fe8701cbe57b5d0b0879f6 NeedsCompilation: yes Package: Mfuzz Version: 2.44.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 6e1c8d489ab1865140d579655cf696f2 NeedsCompilation: no Package: MGFM Version: 1.18.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: a59528c30e469dda4121cf7dbcb277e4 NeedsCompilation: no Package: MGFR Version: 1.10.1 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 197cb5163c956de03ce1896f526a5903 NeedsCompilation: no Package: mgsa Version: 1.32.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 2ac224cf9bb013adc8ede543a950c658 NeedsCompilation: yes Package: MiChip Version: 1.38.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 6c43bb98c9ed2508386b44e5980c519b NeedsCompilation: no Package: microbiome Version: 1.6.0 Depends: R (>= 3.3.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 2f87ce1db908d6621fd4bfc97b8c6225 NeedsCompilation: no Package: microRNA Version: 1.42.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 14fbaf24634fc9b16f8a05ed579f43eb NeedsCompilation: yes Package: MIGSA Version: 1.8.1 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils, vegan Suggests: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, MIGSAdata License: GPL (>= 2) MD5sum: 6a90cb21a907b61533aaae1f7535050f NeedsCompilation: no Package: mimager Version: 1.8.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 44be4c0b62ff306350b691c2518863bb NeedsCompilation: no Package: MIMOSA Version: 1.22.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: Artistic-2.0 MD5sum: e835f0461ae09de0d4a554cc4a5b8b57 NeedsCompilation: yes Package: MineICA Version: 1.24.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 MD5sum: 912b6bf849378551e84ceeda342e31d0 NeedsCompilation: no Package: minet Version: 3.42.0 Imports: infotheo License: file LICENSE MD5sum: 7b93b37bf615c6b55b51095c04d626b8 NeedsCompilation: yes Package: minfi Version: 1.30.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.9.8), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: dacb09fcdb430b4ceb5d60ff816332a7 NeedsCompilation: no Package: MinimumDistance Version: 1.28.0 Depends: R (>= 3.3), VanillaICE (>= 1.31.3) Imports: methods, BiocGenerics, Biobase, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 0.2.0), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: f22446874922f48dd65b7530c1fda2b0 NeedsCompilation: no Package: MiPP Version: 1.56.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 394a2e8f00d6eec273ab9ab6915a5b0b NeedsCompilation: no Package: MIRA Version: 1.6.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 9f9204d9c3afd2c8e0dddd4a82f17853 NeedsCompilation: no Package: MiRaGE Version: 1.26.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 0aa3af0ddc085eee4d4470de1ca2404b NeedsCompilation: no Package: miRBaseConverter Version: 1.8.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) MD5sum: 068113b3bb53e38fd5311719df6895d9 NeedsCompilation: no Package: miRcomp Version: 1.14.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 1de52795a9179f5a582f06f640d37b63 NeedsCompilation: no Package: mirIntegrator Version: 1.14.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: a25c9b60b0e10b2cc870f6ac5ba87118 NeedsCompilation: no Package: miRLAB Version: 1.14.3 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, Roleswitch, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, heatmap.plus, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit License: GPL (>= 2) MD5sum: 29a455fc7a1bad4ea8b08e7d2cbc0cbd NeedsCompilation: no Package: miRmine Version: 1.6.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: db116d76b70324451da0adf8db57b280 NeedsCompilation: no Package: miRNAmeConverter Version: 1.12.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 677abb97b5124109ab30fe667414039f NeedsCompilation: no Package: miRNApath Version: 1.44.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 61d82ff92e3b7025d776598e719eb647 NeedsCompilation: no Package: miRNAtap Version: 1.18.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 8fe90803d5bec9678d94e761e384d2f4 NeedsCompilation: no Package: miRSM Version: 1.2.2 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: ee8cb426297a113cc56ef4f76fbfd8bb NeedsCompilation: yes Package: miRsponge Version: 1.10.0 Depends: R (>= 3.5.0) Imports: corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 55cba888afbd7ad39a0661a38600012e NeedsCompilation: yes Package: miRspongeR Version: 1.10.1 Depends: R (>= 3.5.0) Imports: corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 95e1671b74061b6dd80331147c6bc68d NeedsCompilation: yes Package: Mirsynergy Version: 1.20.0 Depends: R (>= 3.0.2), igraph, ggplot2 Imports: graphics, grDevices, gridExtra, Matrix, parallel, RColorBrewer, reshape, scales, utils Suggests: glmnet, RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: 3acbca5e8024960a4a5cf8d2c85c656b NeedsCompilation: no Package: missMethyl Version: 1.18.0 Depends: R (>= 2.3.0) Imports: limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest, statmod, ruv, stringr, IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db, AnnotationDbi, BiasedUrn, GO.db, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData License: GPL-2 MD5sum: 3c31671ca90e5b59d28e99894fee1e8f NeedsCompilation: no Package: missRows Version: 1.4.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: b6495bc10db157bf9e04d3130d360c99 NeedsCompilation: no Package: mitoODE Version: 1.22.0 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL MD5sum: 99ecb4b674edcc0a17849d5b62105635 NeedsCompilation: yes Package: mixOmics Version: 6.8.5 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: f7a4fc1eb0b1194799b9232d7664442e NeedsCompilation: no Package: MLInterfaces Version: 1.64.1 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, rda, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party Enhances: parallel License: LGPL MD5sum: 90408f0e25fa447247fc959fbc473e41 NeedsCompilation: no Package: mlm4omics Version: 1.2.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats Imports: rstan (>= 2.17.3),rstantools (>= 1.5.0),MASS,Matrix,stats4,ggplot2 LinkingTo: StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0) Suggests: testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 5df4309116903f2eb7418e7fb783fd8e NeedsCompilation: yes Package: MLP Version: 1.32.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 0f025c2156526df2dd6c926f3f9b7820 NeedsCompilation: no Package: MLSeq Version: 2.2.1 Depends: caret, ggplot2 Imports: methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr License: GPL (>= 2) MD5sum: 692c6c7c6042f25c428681642f36dfe7 NeedsCompilation: no Package: MMDiff2 Version: 1.12.0 Depends: R (>= 3.3), Rsamtools, Biobase, Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 79ca696eca801944858d690fba6f6468 NeedsCompilation: no Package: MmPalateMiRNA Version: 1.34.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 MD5sum: f86647e1b79b46ede2ace3a46e7e1109 NeedsCompilation: no Package: mnem Version: 1.0.0 Depends: R (>= 3.6) Imports: cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: c15128027e81bc349db30c15c64ce477 NeedsCompilation: yes Package: MODA Version: 1.10.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 8aea3d81a6f5c87f07d12c96f70cee15 NeedsCompilation: no Package: Modstrings Version: 1.0.3 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, assertive, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 349a818c5d057ab96d04e5680c77a2a9 NeedsCompilation: no Package: MOFA Version: 1.0.0 Depends: R (>= 3.5) Imports: rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2, ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot, ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach, reticulate, grDevices, stats, utils Suggests: knitr, MOFAdata License: LGPL-3 | file LICENSE MD5sum: a117c49e792026198df1770613e3761c NeedsCompilation: yes Package: mogsa Version: 1.18.1 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 215bb7c5ec2b9728a7ddd031190ca810 NeedsCompilation: no Package: monocle Version: 2.12.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: d56a4b34d746a190c68fcb54d4c0dab7 NeedsCompilation: yes Package: MoonlightR Version: 1.10.1 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: b01c0498b7b7fe7d2c2cb77d0732484c NeedsCompilation: no Package: MoPS Version: 1.18.0 Imports: Biobase License: GPL-3 MD5sum: 475aff991362cea8669041b4a8252c3e NeedsCompilation: no Package: mosaics Version: 2.22.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 91e1ae361b6c172d27f265e44b54609e NeedsCompilation: yes Package: motifbreakR Version: 1.14.0 Depends: R (>= 3.2), grid, MotifDb Imports: methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 3dd9087f717dc73dff5223aea9cde251 NeedsCompilation: no Package: motifcounter Version: 1.8.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: b2423266714b75836a8250ebb1a3a0a6 NeedsCompilation: yes Package: MotifDb Version: 1.26.0 Depends: R (>= 3.5.1), methods, BiocGenerics, S4Vectors, IRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: a67c80f80fe5a4c3e4c6f6c56c1fc5cc NeedsCompilation: no Package: motifmatchr Version: 1.6.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: e8538782c56a4cae9ff880a8bcc8ec3d NeedsCompilation: yes Package: motifRG Version: 1.28.0 Depends: R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel, methods, grid, graphics, BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19 Imports: Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector License: Artistic-2.0 MD5sum: c6f8456a1449bf9101aed4ce783e682a NeedsCompilation: no Package: motifStack Version: 1.28.0 Depends: R (>= 2.15.1), methods, grImport2, grid, MotIV, ade4, Biostrings Imports: XML, scales, htmlwidgets,grDevices, stats, stats4, graphics, utils Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr License: GPL (>= 2) MD5sum: 91fbdf0016d23504079d5eb6511cebee NeedsCompilation: no Package: MotIV Version: 1.40.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, S4Vectors, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, utils Suggests: rtracklayer License: GPL-2 MD5sum: f8a64bac15749b7e95f5169c52080c53 NeedsCompilation: yes Package: MPFE Version: 1.20.0 License: GPL (>= 3) MD5sum: 3969c31ce3bb273790779fdc1be3287a NeedsCompilation: no Package: mpra Version: 1.6.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 9d8851deeb9c912a5d31773f7d0a967e NeedsCompilation: no Package: MPRAnalyze Version: 1.2.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: b75748825f109b1050c03ed043f9fe8c NeedsCompilation: no Package: msa Version: 1.16.0 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape, phangorn License: GPL (>= 2) MD5sum: 420454bb8b4b80059f3370245f73a55e NeedsCompilation: yes Package: msgbsR Version: 1.8.0 Depends: R (>= 3.4), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: f69feed2ab2a4927775f9c0eb6d3c029 NeedsCompilation: no Package: MSGFgui Version: 1.18.0 Depends: mzR, xlsx Imports: shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 8ff04d21ba7710e2ee76534fc6915d6b NeedsCompilation: no Package: MSGFplus Version: 1.18.0 Depends: methods Imports: mzID, ProtGenerics Suggests: gWidgets, knitr, testthat License: GPL (>= 2) MD5sum: d05568404d2517ffef6c498d6b559d53 NeedsCompilation: no Package: msmsEDA Version: 1.22.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: aa3ccb1fd5a87df729da090d5ee9b7f4 NeedsCompilation: no Package: msmsTests Version: 1.22.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue License: GPL-2 MD5sum: cbc1d71ad96f24c31683d8f2a4518d15 NeedsCompilation: no Package: MSnbase Version: 2.10.1 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.17.3), S4Vectors, ProtGenerics (>= 1.9.1) Imports: BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: ab8937ed38086b56d6e309363f0c47ed NeedsCompilation: yes Package: MSnID Version: 1.18.1 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR Suggests: BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 616eb099ccfc543bb5dd9a4ce70e3dcf NeedsCompilation: no Package: msPurity Version: 1.10.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite, KEGGREST Suggests: testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA License: GPL (>= 2) MD5sum: 3c75ae8d5c3437d5193646273b393b3c NeedsCompilation: no Package: MSstats Version: 3.16.2 Depends: R (>= 3.6) Imports: lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel, preprocessCore, reshape2, survival, statmod, minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, broom, purrr, stringr, randomForest Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData License: Artistic-2.0 MD5sum: f247c24819ad0e9e7834253f1c27f900 NeedsCompilation: no Package: MSstatsQC Version: 2.2.0 Imports: dplyr,plotly,RecordLinkage,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: e73a4941dde9b2893295400a2a5a46fb NeedsCompilation: no Package: MSstatsQCgui Version: 1.4.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, RecordLinkage, grid Suggests: knitr License: Artistic License 2.0 MD5sum: f1b035376687e76ad64bacf1d269f15b NeedsCompilation: no Package: MSstatsTMT Version: 1.2.7 Depends: R (>= 3.6) Imports: limma, lme4, dplyr, tidyr, nlme, statmod, reshape2, data.table, matrixStats, stats, utils, ggplot2, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 72da7eee27b048b93f6529a7a7b926b7 NeedsCompilation: no Package: MTseeker Version: 1.2.0 Depends: viridis, S4Vectors, GenomeInfoDb, GenomicAlignments, VariantAnnotation Imports: xml2, utils, gmapR, methods, IRanges, Biobase, circlize, jsonlite, graphics, Rsamtools, grDevices, Biostrings, rtracklayer, VariantTools, Homo.sapiens, BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment Suggests: MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2, pkgdown, knitr, rsvg License: GPL-3 MD5sum: e58ce97bc0d80e4200e8830fd9d6bf1b NeedsCompilation: no Package: Mulcom Version: 1.34.1 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 5df71668f986e5628483d150fdee7cf0 NeedsCompilation: yes Package: MultiAssayExperiment Version: 1.10.4 Depends: R (>= 3.6.0), SummarizedExperiment (>= 1.3.81) Imports: methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors (>= 0.17.5), IRanges, Biobase, stats, tidyr, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer License: Artistic-2.0 MD5sum: 6467fe4e78f03cdb2b499add0f928241 NeedsCompilation: no Package: multiClust Version: 1.14.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 0419d9b762cbf770200af0d422ffc92a NeedsCompilation: no Package: MultiDataSet Version: 1.12.0 Depends: R (>= 3.3), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 29d5353058ddf3b0be75aec607c05d7a NeedsCompilation: no Package: multiHiCcompare Version: 1.2.0 Depends: R (>= 3.5.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 4030c762379a976b95076872876bf659 NeedsCompilation: no Package: MultiMed Version: 2.6.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: d9ee95935c15445833065ac51918fd4d NeedsCompilation: no Package: multiMiR Version: 1.6.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: be190b22f4424ab912609f7b5bbcedac NeedsCompilation: no Package: multiOmicsViz Version: 1.8.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: 27efea72517daffda09ad491d7781341 NeedsCompilation: no Package: multiscan Version: 1.44.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 55c6835dbb636b628ea63f5ec1f7bbe8 NeedsCompilation: yes Package: multtest Version: 2.40.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: 9a61cd841ac53057c3019f016535d785 NeedsCompilation: yes Package: muscle Version: 3.26.0 Depends: Biostrings License: Unlimited MD5sum: bd068ea9ecafda73dc59d95186c23cd0 NeedsCompilation: yes Package: MutationalPatterns Version: 1.10.0 Depends: R (>= 3.4.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, parallel, S4Vectors, BiocGenerics (>= 0.18.0), VariantAnnotation (>= 1.18.1), reshape2 (>= 1.4.1), plyr (>= 1.8.3), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), SummarizedExperiment (>= 1.2.2), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2) Suggests: BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5 (>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), testthat License: MIT + file LICENSE MD5sum: 25087f2b88a9828eef9b62ba6245275a NeedsCompilation: no Package: MVCClass Version: 1.58.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: ee30a4d2a083afcff0e7b9c3bd3e7fe6 NeedsCompilation: no Package: MWASTools Version: 1.8.0 Depends: R(>= 3.4) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 6682a0abac0f768907754383a22bd954 NeedsCompilation: no Package: mygene Version: 1.20.0 Depends: R (>= 3.2.1), GenomicFeatures, Imports: httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf, plyr Suggests: BiocStyle License: Artistic-2.0 MD5sum: 0b83f62d78a6c3dca0bfd49c4b4a2abc NeedsCompilation: no Package: myvariant Version: 1.14.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 3fd2a1cd530340e48ed29d1b6a0282fc NeedsCompilation: no Package: mzID Version: 1.22.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: d3b509c2903fedb8bbd5498b7b619159 NeedsCompilation: no Package: mzR Version: 2.18.1 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1), ncdf4 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML License: Artistic-2.0 MD5sum: 56ee30fbaa37970f2caf4357d99621bc NeedsCompilation: yes Package: NADfinder Version: 1.8.1 Depends: R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager License: GPL (>= 2) MD5sum: 967dd5808350103047e5547d03e26c38 NeedsCompilation: no Package: NanoStringDiff Version: 1.14.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 4e7839ffa608368251d100a3177bd495 NeedsCompilation: yes Package: NanoStringQCPro Version: 1.16.0 Depends: R (>= 3.2), methods Imports: AnnotationDbi (>= 1.26.0), org.Hs.eg.db (>= 2.14.0), Biobase (>= 2.24.0), knitr (>= 1.12), NMF (>= 0.20.5), RColorBrewer (>= 1.0-5), png (>= 0.1-7) Suggests: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: a2bf9ee2b3bdfc8baa6e60b24465811d NeedsCompilation: no Package: nanotatoR Version: 1.0.0 Depends: R (>= 3.6) Imports: hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats, grDevices, graphics, stringr, knitr, testthat, utils, AnnotationDbi, httr, org.Hs.eg.db, rtracklayer Suggests: rmarkdown, yaml License: file LICENSE MD5sum: fc74467fa96a2c4329e8494eb6caf9ea NeedsCompilation: no Package: NarrowPeaks Version: 1.28.0 Depends: R (>= 2.10.0), splines Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, fda, CSAR, ICSNP Suggests: rtracklayer, BiocStyle, GenomicRanges, CSAR License: Artistic-2.0 MD5sum: 5964cd4667e6bb6dafba34e392a6b835 NeedsCompilation: yes Package: NBAMSeq Version: 1.0.1 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: 7918fe4d149ab4b9675fe62d8d0f86a6 NeedsCompilation: no Package: NBSplice Version: 1.2.1 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4282dfb4bea9ffe49893c07c97e2b5e7 NeedsCompilation: no Package: ncdfFlow Version: 2.30.1 Depends: R (>= 2.14.0), flowCore(>= 1.45.11), RcppArmadillo, methods, BH Imports: Biobase,BiocGenerics,flowCore,flowViz,zlibbioc LinkingTo: Rcpp,RcppArmadillo,BH, Rhdf5lib Suggests: testthat,parallel License: Artistic-2.0 MD5sum: 559d7f7d0482eb47e056c5fba2311b77 NeedsCompilation: yes Package: NCIgraph Version: 1.32.0 Depends: R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCy3, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 0bcb95b9449cc4451fcf113b5f1a3b10 NeedsCompilation: no Package: ndexr Version: 1.6.1 Depends: igraph Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD MD5sum: 978ce4ab87872f7422cb323d00212784 NeedsCompilation: no Package: NeighborNet Version: 1.2.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: 678c606cc75df11a475c99688a809b11 NeedsCompilation: no Package: nem Version: 2.58.0 Depends: R (>= 3.0) Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod, plotrix, limma Suggests: Biobase (>= 1.10) Enhances: doMC, snow, parallel License: GPL (>= 2) MD5sum: 26c590b60db3f910b797964eba70b38d NeedsCompilation: yes Package: netbenchmark Version: 1.16.0 Depends: grndata (>= 0.99.3) Imports: Rcpp (>= 0.11.0), minet, GENIE3, c3net, PCIT, GeneNet, tools, pracma, Matrix, corpcor, fdrtool LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, knitr, graph License: CC BY-NC-SA 4.0 MD5sum: a1b4608795a70e022d26aa7c5c34a6d2 NeedsCompilation: yes Package: netbiov Version: 1.18.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) MD5sum: ccc0ab1d17b66fabdfa2ea927353e361 NeedsCompilation: no Package: netboost Version: 1.0.0 Depends: R (>= 3.6.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr License: GPL-3 OS_type: unix MD5sum: eca9de5dc79b990dbac1e08f0716492d NeedsCompilation: yes Package: nethet Version: 1.16.1 Imports: glasso, mvtnorm, parcor, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2 Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 5412c0920d7eb6ca174d5d4969ea2cae NeedsCompilation: yes Package: NetPathMiner Version: 1.20.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: b5229cee01ad66180ee86c8a50ee9d03 NeedsCompilation: yes Package: netprioR Version: 1.10.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: a09b310b2afd257aa263df687c15e0c4 NeedsCompilation: no Package: netReg Version: 1.8.0 Depends: R(>= 3.4) Imports: Rcpp, stats LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting License: GPL-3 | BSL-1.0 + file LICENSE MD5sum: 3577e49e7a74fac264e70a907d4834c9 NeedsCompilation: yes Package: netresponse Version: 1.44.0 Depends: R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2 Imports: dmt, ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer License: GPL (>= 2) MD5sum: c0ad8cb4cdef69e676af176c72cf9cac NeedsCompilation: yes Package: NetSAM Version: 1.24.0 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 1.34.0) Imports: methods Suggests: RUnit, BiocGenerics License: LGPL MD5sum: ab2e72fd048e17cd4f19366c2851c433 NeedsCompilation: no Package: netSmooth Version: 1.4.0 Depends: R (>= 3.5), scater (>= 1.9.20), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel License: GPL-3 MD5sum: c53bbdefc35f6169ed76bf30ad1cf686 NeedsCompilation: no Package: networkBMA Version: 2.24.0 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1), leaps LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH License: GPL (>= 2) MD5sum: c4412287f245abd27fad8563da668e11 NeedsCompilation: yes Package: NGScopy Version: 1.17.1 Depends: R (>= 3.1.0) Imports: methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0), changepoint (>= 2.1.1) Suggests: RUnit, NGScopyData, GenomicRanges License: GPL (>= 2) MD5sum: b8b9721f675895d17f74e4a40db36eb2 NeedsCompilation: no Package: ngsReports Version: 1.0.1 Depends: BiocGenerics, ggplot2, tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 0.8.0), ggdendro, grDevices, grid, kableExtra, lubridate, methods, pander, parallel, plotly, readr, reshape2, rmarkdown, Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect (>= 0.2.3), truncnorm, utils, viridisLite, XVector, zoo Suggests: BiocStyle, Cairo, knitr, testthat License: file LICENSE MD5sum: f5109111749aa0fd481f33bf60c07196 NeedsCompilation: no Package: nnNorm Version: 2.48.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: a1dd8fef52c92c47e1bc17ca0fe5c823 NeedsCompilation: no Package: NOISeq Version: 2.28.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 2211009273dbb9def27fab7612bf5ee7 NeedsCompilation: no Package: nondetects Version: 2.14.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: 6ed082936ef8d168c1bb04cb44def8df NeedsCompilation: no Package: normalize450K Version: 1.12.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 28b62cd9b5c4cf1b1e2b02e9043e35fa NeedsCompilation: no Package: NormalyzerDE Version: 1.2.0 Depends: R (>= 3.5) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 670b920cccf0189ef5a6ad4a6bce3988 NeedsCompilation: no Package: NormqPCR Version: 1.30.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 9851470e31655277db61d1a4e42b965e NeedsCompilation: no Package: normr Version: 1.10.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: d7a14e44272acd117020c25ebfccfd08 NeedsCompilation: yes Package: npGSEA Version: 1.20.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: e52fe0ffeaaa40b3e988dd4550f99052 NeedsCompilation: no Package: NTW Version: 1.34.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: e76680fac1736cf1e010febd204d5300 NeedsCompilation: no Package: nucleoSim Version: 1.12.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: a7c5dacf53ecce0dd78991928b9656c5 NeedsCompilation: no Package: nucleR Version: 2.16.0 Depends: methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 03152cac4449fffd5ebda5bc4f2fa849 NeedsCompilation: no Package: nuCpos Version: 1.2.0 Depends: R (>= 3.5.1) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: 8ae37dce2a611262d22eb1fe3c7dfb15 NeedsCompilation: yes Package: NuPoP Version: 1.34.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 2f2469ea1cc2c7a36a3ebe6abc8cfe28 NeedsCompilation: yes Package: occugene Version: 1.44.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: f962202fd42a1aa9933fe50bacbdef7d NeedsCompilation: no Package: OCplus Version: 1.58.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL MD5sum: 67aa4e3c2f906fb79a70714819df5e13 NeedsCompilation: no Package: odseq Version: 1.12.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: 7b25fb80682d5695daa2562bafa1987d NeedsCompilation: no Package: OGSA Version: 1.14.0 Depends: R (>= 3.2.0) Imports: gplots(>= 2.8.0), limma(>= 3.18.13), Biobase License: GPL (== 2) MD5sum: ea8ef4b05643bef784d87d23ffa04d50 NeedsCompilation: no Package: oligo Version: 1.48.0 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt, AnnotationDbi, GenomeGraphs, RCurl Enhances: ff, doMC, doMPI License: LGPL (>= 2) MD5sum: d0d6c5b97dfe4ab1811da5c58d3cad1b NeedsCompilation: yes Package: oligoClasses Version: 1.46.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: f7ddb837c47f2126caea204d7cf0deb5 NeedsCompilation: no Package: OLIN Version: 1.62.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 3853f23caccdf30142ec1c85b4d9a47b NeedsCompilation: no Package: OLINgui Version: 1.58.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: de501564169222861b7036ba2516ad07 NeedsCompilation: no Package: OmaDB Version: 2.0.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 04d5c2a7123cc04e31e0a3c4c0f8eac2 NeedsCompilation: no Package: omicade4 Version: 1.24.1 Depends: R (>= 3.0.0), ade4 Imports: made4 Suggests: BiocStyle License: GPL-2 MD5sum: 4f693891d6b1843afaa614b19ce43276 NeedsCompilation: no Package: OmicCircos Version: 1.22.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 9d3312b4108c9266549045b04bbdba88 NeedsCompilation: no Package: omicplotR Version: 1.4.3 Depends: R (>= 3.5) Imports: ALDEx2 (>= 1.8.0), compositions, grDevices, knitr, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 16a4c5073efc59688c9d166802b4d0de NeedsCompilation: no Package: omicRexposome Version: 1.6.0 Depends: R (>= 3.4), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: b6f376d1a54b397d8ae243ecdfe6142b NeedsCompilation: no Package: OmicsLonDA Version: 1.0.0 Depends: R(>= 3.6) Imports: SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2, BiocParallel, parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: f67896a0ef0785819dc9642850235b15 NeedsCompilation: no Package: OmicsMarkeR Version: 1.16.0 Depends: R (>= 3.2.0) Imports: graphics, stats, utils, plyr (>= 1.8), data.table (>= 1.9.4), caret (>= 6.0-37), DiscriMiner (>= 0.1-29), e1071 (>= 1.6-1), randomForest (>= 4.6-10), gbm (>= 2.1), pamr (>= 1.54.1), glmnet (>= 1.9-5), caTools (>= 1.14), foreach (>= 1.4.1), permute (>= 0.7-0), assertive (>= 0.3-0), assertive.base (>= 0.0-1) Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 9c82a60dce4f945966d2ba6fd761ecb3 NeedsCompilation: no Package: OMICsPCA Version: 1.2.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: e69ae22e13ed95a9060126f90b5ecbd0 NeedsCompilation: no Package: omicsPrint Version: 1.4.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: 2021c5dae6aac2e7d35b1ddafe15135c NeedsCompilation: no Package: Onassis Version: 1.6.1 Depends: R (>= 3.4), rJava, OnassisJavaLibs Imports: GEOmetadb, RSQLite, data.table, methods, tools, utils, AnnotationDbi, RCurl, stats, DT, data.table, knitr Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra License: GPL-2 MD5sum: fbe89471fe2000b56fdc116754c786d4 NeedsCompilation: no Package: oncomix Version: 1.6.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: dc2814bcbc50ab49ba1b907cddb72e40 NeedsCompilation: no Package: OncoScore Version: 1.12.0 Depends: R (>= 3.6), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: bdf73cdd63364222c25bc2da53f68684 NeedsCompilation: no Package: OncoSimulR Version: 2.14.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, nem LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: ad7ec9aa5aa85b0e0c961a23adf441ab NeedsCompilation: yes Package: oneSENSE Version: 1.6.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 54a7031cad9942f3de0ced671a2e7c5c NeedsCompilation: no Package: onlineFDR Version: 1.2.0 Imports: stats Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8c0cc1ff5c7853c657c14a291fa3c130 NeedsCompilation: no Package: ontoProc Version: 1.6.0 Depends: R (>= 3.5), ontologyIndex Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle License: Artistic-2.0 MD5sum: 1339c7f7b63ecf3a629765e8ba2c5a1a NeedsCompilation: no Package: openCyto Version: 1.22.2 Depends: flowWorkspace(>= 3.31.8) Imports: methods,Biobase,BiocGenerics,gtools,flowCore(>= 1.31.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace,flowStats(>= 3.29.1),flowClust(>= 3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils LinkingTo: Rcpp Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML License: Artistic-2.0 MD5sum: 56aa419ec24bf7facf91542149601ebb NeedsCompilation: yes Package: openPrimeR Version: 1.6.0 Depends: R (>= 3.4.0) Imports: Biostrings (>= 2.38.4), XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), distr (>= 2.6), distrEx (>= 2.6), fitdistrplus (>= 1.0-7), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0), tinytex (>= 0.5) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: a46cb62bd821bd0381698fa8d3adf64c NeedsCompilation: no Package: openPrimeRui Version: 1.6.0 Depends: R (>= 3.4.0), openPrimeR (>= 0.99.0) Imports: shiny (>= 1.0.2), shinyjs (>= 0.9), shinyBS (>= 0.61), DT (>= 0.2), rmarkdown (>= 1.0) Suggests: knitr (>= 1.13) License: GPL-2 MD5sum: 64ce3b33f1750ddd769caa1f01686597 NeedsCompilation: no Package: oposSOM Version: 2.2.0 Depends: R (>= 3.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: b92d8034deb4e699e0da43859bc42378 NeedsCompilation: yes Package: oppar Version: 1.12.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: c2cdab3611fa027800da04b13fc75da6 NeedsCompilation: yes Package: OPWeight Version: 1.6.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 4472bf693a02a5fc0225ab8c6a741881 NeedsCompilation: no Package: OrderedList Version: 1.56.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) MD5sum: 80f6759e6648c53a1979233a4dd0a7b4 NeedsCompilation: no Package: ORFik Version: 1.4.1 Depends: R (>= 3.6.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: S4Vectors (>= 0.21.3), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), AnnotationDbi (>= 1.45.0), rtracklayer (>= 1.43.0), Rcpp (>= 1.0.0), data.table (>= 1.11.8), Biostrings (>= 2.51.1), stats, tools, Rsamtools (>= 1.35.0), BiocGenerics (>= 0.29.1), ggplot2 (>= 2.2.1), methods (>= 3.6.0) LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 3f23cbc53a12e92a3a9311d971600ba3 NeedsCompilation: yes Package: Organism.dplyr Version: 1.12.1 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, methods, tools, utils, BiocFileCache, DBI, dbplyr Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 20bbcbbcfda52d6d5a83b85a90a493eb NeedsCompilation: no Package: OrganismDbi Version: 1.26.0 Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.23.31) Imports: Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB License: Artistic-2.0 MD5sum: c0f1638c0a1fe72f968933fd0877c3a9 NeedsCompilation: no Package: OSAT Version: 1.32.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: d3f00e9577e4ec4149a4f5f568d7ad4e NeedsCompilation: no Package: Oscope Version: 1.14.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 25588131ddda3404c7e1c1674c9f486c NeedsCompilation: no Package: OTUbase Version: 1.34.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: cb91122e96e990e5975138ff36d21c7f NeedsCompilation: no Package: OutlierD Version: 1.48.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) MD5sum: 44a6e07c906fa063969f5544505ca011 NeedsCompilation: no Package: OUTRIDER Version: 1.2.4 Depends: R (>= 3.4), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, Biobase, BiocGenerics, compiler, DESeq2 (>= 1.16.1), GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, gplots, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, S4Vectors, scales, splines, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr License: MIT + file LICENSE MD5sum: be0ac37cbecd3c55a800a99673e7c923 NeedsCompilation: yes Package: OVESEG Version: 1.0.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 046a686ab8c0f5679692f8899b8a8c25 NeedsCompilation: yes Package: PAA Version: 1.18.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 88bae0739cd3c1eb902e07a2ae2a2d10 NeedsCompilation: yes Package: PADOG Version: 1.26.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGG.db, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: b3d4cf132c70bf0ce99691aabcf0ea3e NeedsCompilation: no Package: PAIRADISE Version: 1.0.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: d394254a019c201f6b9bc6e5490bd29c NeedsCompilation: no Package: paircompviz Version: 1.22.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: b52ac2a27612f5ea60289601fac42af3 NeedsCompilation: no Package: pandaR Version: 1.16.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr License: GPL-2 MD5sum: dc76ba50e9307fd00be88cfc5a8eae54 NeedsCompilation: no Package: panelcn.mops Version: 1.6.1 Depends: R (>= 3.4), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) MD5sum: 89057cd34a815b3eb45be673e3532714 NeedsCompilation: no Package: panp Version: 1.54.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: 9f78631585e785d969cbc4f2035a2083 NeedsCompilation: no Package: PANR Version: 1.30.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: 0a7ad116627065730fe5473064cd5f81 NeedsCompilation: no Package: PanVizGenerator Version: 1.12.0 Depends: methods Imports: shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, digest License: GPL (>= 2) MD5sum: 68fb5e9658c0cc6fab0a3eb8aea62fec NeedsCompilation: no Package: PAPi Version: 1.24.0 Depends: R (>= 2.15.2), svDialogs, KEGGREST License: GPL (>= 2) MD5sum: 196bdffd32b72380c9e610b615c765ae NeedsCompilation: no Package: parglms Version: 1.16.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gQTLBase, gQTLstats, geuvStore2, gwascat, BiocStyle License: Artistic-2.0 MD5sum: 0494730840ec5e71ff1a444532edfc65 NeedsCompilation: no Package: parody Version: 1.42.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 MD5sum: d3707ed299e935718c26f52a37fb2d00 NeedsCompilation: no Package: PAST Version: 1.0.1 Depends: R (>= 3.6) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2 Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: 9e272e355fc1545ba40927bbe54d4654 NeedsCompilation: no Package: Path2PPI Version: 1.14.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: fb9995b5286c70abba1ec04d9331358d NeedsCompilation: no Package: pathifier Version: 1.22.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 MD5sum: 58df0dff57cf54fd9a4cd0f21f13157b NeedsCompilation: no Package: PathNet Version: 1.23.0 Depends: R (>= 1.14.0) Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: 8379b86eac97f490fe40f90d7dcae045 NeedsCompilation: no Package: PathoStat Version: 1.10.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 39aa70d559ca8ed7159ea9fefeab67db NeedsCompilation: no Package: pathprint Version: 1.14.0 Depends: R (>= 3.4) Imports: stats, utils Suggests: ALL, GEOquery, pathprintGEOData, SummarizedExperiment License: GPL MD5sum: f78e3b730d7c273fea0d23ad7c350461 NeedsCompilation: no Package: pathRender Version: 1.52.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 74527eae51dd579c3d27e1c8c15d6932 NeedsCompilation: no Package: pathVar Version: 1.14.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) MD5sum: bb2379f993f3a1fa95240838df6b739e NeedsCompilation: no Package: pathview Version: 1.24.0 Depends: R (>= 2.10), org.Hs.eg.db Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 9b6dd193eb8566c7991ca16a95913f45 NeedsCompilation: no Package: pathwayPCA Version: 1.0.0 Depends: R (>= 3.6) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: d71f4103f7a8b57c8c57c05e616587dd NeedsCompilation: no Package: PathwaySplice Version: 1.8.0 Depends: R (>= 3.5.0) Imports: goseq, Biobase, DOSE, reshape2, igraph, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, AnnotationDbi, JunctionSeq, BiasedUrn, GO.db,gdata, geneLenDataBase, grDevices, graphics, stats, utils, VennDiagram, RColorBrewer, ensembldb, AnnotationHub, S4Vectors, dplyr, plotly, webshot, htmlwidgets , mgcv ,gridExtra, grid ,gplots, tibble , EnrichmentBrowser, annotate , KEGGREST Suggests: testthat, knitr, rmarkdown License: LGPL (>= 2) MD5sum: 039776737311855f25e984c72c6bebaa NeedsCompilation: no Package: paxtoolsr Version: 1.18.0 Depends: R (>= 3.2), rJava (>= 0.9-8), XML Imports: utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr Suggests: testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel, org.Hs.eg.db License: LGPL-3 MD5sum: 3652a8dd52b4f53044e378ad85457550 NeedsCompilation: no Package: Pbase Version: 0.24.0 Depends: R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz Imports: cleaver (>= 1.3.6), Biobase, Biostrings (>= 2.47.5), IRanges (>= 2.13.11), S4Vectors (>= 0.17.24), mzID, mzR (>= 1.99.1), MSnbase (>= 1.15.5), Pviz, biomaRt, GenomicRanges (>= 1.31.7), rtracklayer (>= 1.39.6), ensembldb (>= 1.99.13), BiocParallel, AnnotationFilter Suggests: testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86 (>= 2.0.0) License: GPL-3 MD5sum: 76e54fdaedbffd9c9fd04a08529b0519 NeedsCompilation: no Package: pcaExplorer Version: 2.10.1 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), d3heatmap, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: 23cf938547836ffe2d81afad68af218e NeedsCompilation: no Package: pcaGoPromoter Version: 1.28.0 Depends: R (>= 2.14.0), ellipse, Biostrings Imports: AnnotationDbi Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel License: GPL (>= 2) MD5sum: da4aa4bf501174c978b6f2718e2d32ae NeedsCompilation: no Package: pcaMethods Version: 1.76.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 999fb2811e2fff2da737fa969cf809fd NeedsCompilation: yes Package: PCAN Version: 1.12.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: f1232cbd6da8413cc00d752f91521c1b NeedsCompilation: no Package: PCAtools Version: 1.0.0 Depends: stats, ggplot2, ggrepel, reshape2, lattice, grDevices, cowplot Suggests: RUnit, BiocGenerics, knitr, Biobase, GEOquery, biomaRt, ggplotify License: GPL-3 MD5sum: 6ef2bff3637161a072efc798a8fb2af9 NeedsCompilation: no Package: pcot2 Version: 1.52.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) MD5sum: 140130ec124351e324200761b14f98d0 NeedsCompilation: no Package: PCpheno Version: 1.46.0 Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4 Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 9d57cab88fccbf8ec5ff40dcb0923125 NeedsCompilation: no Package: pcxn Version: 2.6.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 7354db0c5ff6dfe33eba1ca08d943360 NeedsCompilation: no Package: pdInfoBuilder Version: 1.48.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: 49c010d594178513df2396a1a0b69fb2 NeedsCompilation: yes Package: PECA Version: 1.20.0 Depends: R (>= 3.3) Imports: ROTS, limma, affy, genefilter, preprocessCore, aroma.affymetrix, aroma.core Suggests: SpikeIn License: GPL (>= 2) MD5sum: b0a710433143e3c8529b31953dd75096 NeedsCompilation: no Package: PepsNMR Version: 1.2.1 Depends: R (>= 3.5) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: a7651de5219e8a045f9f11280b59e07d NeedsCompilation: no Package: pepStat Version: 1.18.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: e78ab9a2f6eb8002061befa6ff303c68 NeedsCompilation: no Package: pepXMLTab Version: 1.18.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 602907c5343bbd61c7b0692fe5ad9202 NeedsCompilation: no Package: perturbatr Version: 1.4.0 Depends: R (>= 3.5), methods, stats Imports: dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph, foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid, utils, graphics, scales, magrittr, formula.tools, rlang Suggests: testthat, lintr, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: dcc3d7550c1dd7cfdd7d36e972ffc36d NeedsCompilation: no Package: PGA Version: 1.14.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges, Biostrings (>= 2.26.3), data.table, rTANDEM Imports: S4Vectors (>= 0.9.25), Rsamtools (>= 1.10.2), GenomicFeatures (>= 1.19.8), biomaRt (>= 2.17.1), stringr, RCurl, Nozzle.R1, VariantAnnotation (>= 1.7.28), rtracklayer, RSQLite, ggplot2, AnnotationDbi, customProDB (>= 1.21.5), pheatmap Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils License: GPL-2 MD5sum: b2a21d6f3de2c4b7472feffcc39067fa NeedsCompilation: no Package: pgca Version: 1.8.0 Imports: utils, stats Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 0294ac9de15c3e72b20f63e3dfa2ea46 NeedsCompilation: no Package: PGSEA Version: 1.58.0 Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 MD5sum: 93b85788807b8e3a877613edb930b59d NeedsCompilation: no Package: phantasus Version: 1.4.0 Depends: R (>= 3.5) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, Matrix.utils, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table License: MIT + file LICENSE MD5sum: 7baaeca928110d421ce44d191994569e NeedsCompilation: no Package: PharmacoGx Version: 1.14.2 Depends: R (>= 3.6) Imports: Biobase, piano, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, lsa, reshape2 Suggests: xtable, testthat License: Artistic-2.0 MD5sum: 36b962afa9ad1af9980c609df82efbc6 NeedsCompilation: no Package: phemd Version: 1.0.1 Depends: R (>= 3.6), monocle Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase Suggests: knitr License: GPL-2 MD5sum: 4792170112226f102cb2914b77161e88 NeedsCompilation: no Package: phenopath Version: 1.8.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 85a6e099b86c2fa0a42f319fbc937ae8 NeedsCompilation: yes Package: phenoTest Version: 1.32.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2 Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 61f3a068e4988e693f6f2858030b0d02 NeedsCompilation: no Package: PhenStat Version: 2.20.3 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: ddc3f35510b416c3bfab46c8b43e3bf6 NeedsCompilation: no Package: philr Version: 1.10.1 Imports: ape, phangorn, tidyr, ggplot2, ggtree Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr License: GPL-3 MD5sum: eed8b4b7216fb64d8424ecda707a79c2 NeedsCompilation: no Package: phosphonormalizer Version: 1.8.0 Depends: R (>= 3.4.0) Imports: plyr, stats, graphics, matrixStats Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: cb886d2ef9235727c1ceeb53324493de NeedsCompilation: no Package: phyloseq Version: 1.28.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7.4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5) Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Enhances: doParallel (>= 1.0.10) License: AGPL-3 MD5sum: e335968eb4f632162cb6a177117c8cf0 NeedsCompilation: no Package: Pi Version: 1.12.0 Depends: XGR, igraph, dnet, ggplot2, graphics Imports: Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice, caret, plot3D, stats Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview, tidyr, dplyr License: GPL-3 MD5sum: 5d4c183ea18ca8fb9483a0c78f753d79 NeedsCompilation: no Package: piano Version: 2.0.2 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 9171d8e0585315bbf3073f33ac389832 NeedsCompilation: no Package: pickgene Version: 1.56.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 3e07394aaa3cf494b93d00b7307bda59 NeedsCompilation: no Package: PICS Version: 2.28.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats, Rsamtools, GenomicAlignments, S4Vectors Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 MD5sum: e0ebcad166db4df73d197dc69be40893 NeedsCompilation: yes Package: Pigengene Version: 1.10.0 Depends: R (>= 3.3.0), graph Imports: bnlearn (>= 4.4.1), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8) Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, BiocStyle, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 08665f7c9021ef0176f685b864986b92 NeedsCompilation: no Package: PING Version: 2.28.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: 26cf6d98525f5454eb6aad179efb0063 NeedsCompilation: yes Package: pint Version: 1.34.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: BSD_2_clause + file LICENSE MD5sum: be40bec1406b1a9a9c2d208e7277a2d4 NeedsCompilation: no Package: pipeFrame Version: 1.0.0 Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils Suggests: BiocManager, knitr, rtracklayer, testthat License: GPL-3 MD5sum: bc92296ebc9ad5fb1438ee41a753d1e3 NeedsCompilation: no Package: pkgDepTools Version: 1.50.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocManager License: GPL-2 MD5sum: a94aca53e28b9b9f8f3835295c17aa12 NeedsCompilation: no Package: plateCore Version: 1.41.1 Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils, flowStats Suggests: gplots License: Artistic-2.0 MD5sum: 06081e7ebf7b8136766ba03420f1a2da NeedsCompilation: no Package: plethy Version: 1.22.0 Depends: R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1), BiocGenerics, S4Vectors Imports: Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2, Biobase Suggests: RUnit, BiocStyle License: GPL-3 MD5sum: 602fa867af93cc7b3635b972b4aa16e9 NeedsCompilation: no Package: plgem Version: 1.56.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS License: GPL-2 MD5sum: 790c2aa391353fcfe65940c349b1f31e NeedsCompilation: no Package: plier Version: 1.54.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: cccc4742ee3ce9dfcd187b955cd91b16 NeedsCompilation: yes Package: plotGrouper Version: 1.2.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: a6c7449cf43ca43eea040a1288c1432d NeedsCompilation: no Package: PLPE Version: 1.44.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: d2deab4a268dc342757b63a8d4645700 NeedsCompilation: no Package: plrs Version: 1.24.0 Depends: R (>= 2.10), Biobase Imports: BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray, methods, quadprog, Rcsdp, stats, stats4, utils Suggests: mvtnorm, methods License: GPL (>= 2.0) MD5sum: 8b386b7ca4465d74f79d9e67002c6f2a NeedsCompilation: no Package: plw Version: 1.44.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 MD5sum: 9817b3abce8d6597da3ce7584cb04807 NeedsCompilation: yes Package: plyranges Version: 1.4.4 Depends: R (>= 3.5), methods, BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4) Imports: dplyr, rlang (>= 0.2.0), magrittr, tidyselect, rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>= 0.17.41), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, ggplot2, HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr License: Artistic-2.0 MD5sum: 68eac8d329b81f1290d874606ec2b145 NeedsCompilation: no Package: pmm Version: 1.16.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: cfed0aed28aaae52afda91973a26487a NeedsCompilation: no Package: podkat Version: 1.16.0 Depends: R (>= 3.2.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: 679979f4046c4e43e81d953f250091fb NeedsCompilation: yes Package: pogos Version: 1.4.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat License: Artistic-2.0 MD5sum: c5c65f17d311d12b7c8725f16ae7941d NeedsCompilation: no Package: polyester Version: 1.20.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown License: Artistic-2.0 MD5sum: 7e80f66d0d4d869281a4ad04764594b9 NeedsCompilation: no Package: Polyfit Version: 1.18.0 Depends: DESeq Suggests: BiocStyle License: GPL (>= 3) MD5sum: 34ca445df2af6dcabf24929bd126a6d2 NeedsCompilation: no Package: POST Version: 1.8.0 Depends: R (>= 3.4.0) Imports: stats, CompQuadForm, Matrix, survival, Biobase, GSEABase License: GPL (>= 2) MD5sum: c46f4319e91a8ac8655003ed8ff437bc NeedsCompilation: no Package: PoTRA Version: 1.0.0 Depends: R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph, graph, graphite Suggests: BiocStyle, knitr, rmarkdown, colr, metap, repmis License: LGPL MD5sum: 28dd409c781102ceb5ea0088be879397 NeedsCompilation: no Package: PowerExplorer Version: 1.4.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: DESeq2, ROTS, vsn, stats, utils, methods, gridExtra, MASS, data.table, ggplot2, Biobase, S4Vectors, BiocParallel Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 9327ee552a02d059fa9f4efe1d0a816e NeedsCompilation: no Package: powerTCR Version: 1.4.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, tcR, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: ad42fe5c1066c24b604c06bc70370584 NeedsCompilation: no Package: PPInfer Version: 1.10.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData License: Artistic-2.0 MD5sum: c9394e3414d3dd3f12878b6513c77a42 NeedsCompilation: no Package: ppiStats Version: 1.50.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.19) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 MD5sum: 3e33c457efd15516f13d7f8144e76709 NeedsCompilation: no Package: pqsfinder Version: 2.0.2 Depends: Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.69.0) Suggests: BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 7106d250e161b891c4300fa88ed93f04 NeedsCompilation: yes Package: prada Version: 1.60.0 Depends: R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS2, tcltk License: LGPL MD5sum: bdb750f5fd7eee86f2189acc886dc394 NeedsCompilation: yes Package: pram Version: 1.0.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: bb7c3664804776014818ec6c3c14187b NeedsCompilation: no Package: prebs Version: 1.24.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: c71c6d8ff29857fbdfd7ccd9e8986313 NeedsCompilation: no Package: PrecisionTrialDrawer Version: 1.0.1 Depends: R (>= 3.6) Imports: graphics, grDevices, stats, utils, methods, cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer, BiocParallel, magrittr, biomaRt, XML, httr, jsonlite, ggplot2, ggrepel, grid, S4Vectors, IRanges, GenomicRanges, LowMACAAnnotation, googleVis, shiny, shinyBS, DT, brglm, matrixStats Suggests: BiocStyle, knitr, rmarkdown, dplyr License: GPL-3 MD5sum: e4334116cfb626bc7fe77a460255628f NeedsCompilation: no Package: PREDA Version: 1.30.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 MD5sum: df5582ae2251f2f67890132053c1104e NeedsCompilation: no Package: predictionet Version: 1.30.0 Depends: igraph, catnet Imports: penalized, RBGL, MASS Suggests: network, minet, knitr License: Artistic-2.0 MD5sum: 38a12700b0f4e71deaecacb35555b12c NeedsCompilation: yes Package: preprocessCore Version: 1.46.0 Imports: stats License: LGPL (>= 2) MD5sum: 898d22c5820f39234dd575ae4f46631f NeedsCompilation: yes Package: primirTSS Version: 1.2.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: d01f813dec836a5a410b486e9957186f NeedsCompilation: no Package: PrInCE Version: 1.0.1 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 1ffe4a946f6fa4e9549693ec41fb0d88 NeedsCompilation: no Package: Prize Version: 1.14.0 Imports: diagram, stringr, ggplot2, reshape2, grDevices, matrixcalc, stats, gplots, methods, utils, graphics Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e9227d878c72a4eb9b1a2757566f0755 NeedsCompilation: no Package: proBAMr Version: 1.18.0 Depends: R (>= 3.0.1), IRanges, AnnotationDbi Imports: GenomicRanges, Biostrings, GenomicFeatures, rtracklayer Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e6c06b72cd2b79acefe5811234f8b0d4 NeedsCompilation: no Package: proBatch Version: 1.0.0 Depends: R (>= 3.6) Imports: Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2, grDevices, lazyeval, lubridate, magrittr, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, readr, reshape2, rlang, scales, viridis, stats, sva, tidyr, tibble, utils, wesanderson, WGCNA Suggests: knitr, rmarkdown, devtools, roxygen2, testthat License: GPL-3 MD5sum: 44e29aaeccc43d5683608c7a5acb32ea NeedsCompilation: no Package: PROcess Version: 1.60.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 MD5sum: 491d0d87b6f78d90fb63e97754e31e21 NeedsCompilation: no Package: procoil Version: 2.12.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) MD5sum: 728915d86c49b2a50f60bc7b44f5fa2c NeedsCompilation: no Package: proFIA Version: 1.10.0 Depends: R (>= 2.5.0), xcms Imports: stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls Suggests: BiocGenerics, plasFIA, knitr, License: CeCILL MD5sum: dbd75f01b57a3e7dd6116f621d4a4cfa NeedsCompilation: yes Package: profileplyr Version: 1.0.1 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools, ggplot2 License: GPL (>= 3) MD5sum: b920fc3703909b98dd0a06e3ee072fea NeedsCompilation: no Package: profileScoreDist Version: 1.12.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE MD5sum: a188b68fbaee0c0d2f85da954c5ae4e6 NeedsCompilation: yes Package: progeny Version: 1.6.0 Depends: R (>= 3.4.0) Imports: Biobase Suggests: airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl License: Apache License (== 2.0) | file LICENSE MD5sum: e0365039dc839c386095ce036ebf39d6 NeedsCompilation: no Package: projectR Version: 1.0.0 Imports: methods, cluster, stats, limma, CoGAPS, NMF, ROCR Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, viridis, ggplot2 License: GPL (== 2) MD5sum: d483de0763d074a224b9189620ad65a8 NeedsCompilation: no Package: pRoloc Version: 1.24.1 Depends: R (>= 2.15), MSnbase (>= 1.19.20), MLInterfaces (>= 1.37.1), methods, Rcpp (>= 0.10.3), BiocParallel Imports: Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape License: GPL-2 MD5sum: 4d667224c830a34dc8216804b427cadc NeedsCompilation: yes Package: pRolocGUI Version: 1.18.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.11.1), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2 Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown License: GPL-2 MD5sum: b399020af3773548f3e8e4a4375058ec NeedsCompilation: no Package: PROMISE Version: 1.36.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: deab13ebe8ec088e9585aa2291557a4b NeedsCompilation: no Package: PROPER Version: 1.16.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq,DSS,knitr License: GPL MD5sum: f1e52dedad4eca5991a82a7f828ddc18 NeedsCompilation: no Package: PROPS Version: 1.6.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 6883deadd0520221e162f777a595af90 NeedsCompilation: no Package: Prostar Version: 1.16.10 Depends: R (>= 3.6) Imports: DAPAR (>= 1.16.11), DAPARdata (>= 1.14.0), rhandsontable, data.table, shinyjs, DT, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, R.utils, shinythemes, XML,later, shinycssloaders, future, promises, colourpicker, BiocManager, shinyjqui,shinyTree, shinyWidgets Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 644e66768a3528b760d8c79ab41fb5e1 NeedsCompilation: no Package: proteinProfiles Version: 1.24.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: 1fa0f4040fd773e2b93b140148d2158e NeedsCompilation: no Package: ProteomicsAnnotationHubData Version: 1.14.0 Depends: AnnotationHub (>= 2.1.45), AnnotationHubData, Imports: mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils, Biobase, BiocManager, RCurl Suggests: knitr, BiocStyle, rmarkdown, testthat License: Artistic-2.0 MD5sum: 64ec92b50e7965a36c7097de7a946814 NeedsCompilation: no Package: ProteoMM Version: 1.2.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: 39878649f2415502a7e23ec22f732fa6 NeedsCompilation: no Package: proteoQC Version: 1.20.0 Depends: R (>= 3.0.0), XML, VennDiagram, MSnbase Imports: rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel, rpx, tidyr, dplyr, plotly, rmarkdown, Suggests: RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics License: LGPL-2 MD5sum: d4e2ae9b7a83e7ca71e5f416a8b44d55 NeedsCompilation: no Package: ProtGenerics Version: 1.16.0 Depends: methods License: Artistic-2.0 MD5sum: e2315c50a88dfbfb1c3c9232bde4f6ce NeedsCompilation: no Package: PSEA Version: 1.18.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 MD5sum: c33029fffd8410028cf1e4cf81a2259d NeedsCompilation: no Package: psichomics Version: 1.10.2 Depends: R (>= 3.5), shiny (>= 1.0.3), shinyBS Imports: AnnotationDbi, AnnotationHub, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods, org.Hs.eg.db LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi License: MIT + file LICENSE MD5sum: a658f163e121733fd3b50943cde63457 NeedsCompilation: yes Package: PSICQUIC Version: 1.22.2 Depends: R (>= 3.2.2), methods, IRanges, biomaRt (>= 2.34.1), BiocGenerics, httr, plyr Imports: RCurl Suggests: org.Hs.eg.db License: Apache License 2.0 MD5sum: 5bbdb85d0c0856784ed1b8d084d16540 NeedsCompilation: no Package: psygenet2r Version: 1.16.0 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, BiocManager, Biobase, labeling, GO.db Suggests: testthat, knitr License: MIT + file LICENSE MD5sum: d2c4b6390dd4574a02d4e6ccc50ee6b5 NeedsCompilation: no Package: puma Version: 3.26.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 3f6c478de9518b82f635da32011d1455 NeedsCompilation: yes Package: PureCN Version: 1.14.3 Depends: R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, rhdf5, Matrix Suggests: PSCBS, copynumber, BiocStyle, BiocParallel, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat License: Artistic-2.0 MD5sum: df042474daaeda383bb16c6a71bb4eed NeedsCompilation: no Package: pvac Version: 1.32.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: fe0195602ae0184096ea60fecc37be75 NeedsCompilation: no Package: pvca Version: 1.24.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 5977112497ca22656df168911b6fcbc1 NeedsCompilation: no Package: Pviz Version: 1.18.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 699bc1eefaddda38bed03d0226c36ddd NeedsCompilation: no Package: PWMEnrich Version: 4.20.0 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 4cf6c371eaf391c0c888b5aec6eeb739 NeedsCompilation: no Package: pwOmics Version: 1.16.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz License: GPL (>= 2) MD5sum: b37d8682715801a50d85e8e06446a7bf NeedsCompilation: no Package: qckitfastq Version: 1.0.1 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: c4039649539e600c32755648840b8623 NeedsCompilation: yes Package: qcmetrics Version: 1.22.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle License: GPL-2 MD5sum: 58dc1a2e6afca43f5d883fdde8d1282b NeedsCompilation: no Package: QDNAseq Version: 1.20.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.50.2), R.utils (>= 2.3.0), Rsamtools (>= 1.20), BiocParallel (>= 1.6.6), Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.8), GenomeInfoDb (>= 1.6.0), future (>= 0.14.0), R.cache (>= 0.12.0) License: GPL MD5sum: 9a6c7d92574ef0f22d4742de20100cfa NeedsCompilation: no Package: qpcrNorm Version: 1.42.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: 49976aed28892f2c1e3c62c86f42d9e7 NeedsCompilation: no Package: qpgraph Version: 2.18.0 Depends: R (>= 3.4) Imports: methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 336334ed0593d42313616e0fd7800c48 NeedsCompilation: yes Package: qPLEXanalyzer Version: 1.2.0 Depends: R (>= 3.6), Biobase, statmod, MSnbase Imports: tidyr, preprocessCore, limma, ggplot2, RColorBrewer, stats, utils, Biostrings, GenomicRanges, IRanges, graphics, BiocGenerics, stringr, purrr, tibble, ggdendro, grDevices, dplyr, magrittr, assertthat Suggests: UniProt.ws, knitr, qPLEXdata License: GPL-2 MD5sum: fc7302cc24a8bd83209303b4b3951950 NeedsCompilation: no Package: qrqc Version: 1.38.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rhtslib (>= 1.15.3) License: GPL (>= 2) MD5sum: d1614dbf5b895a83baf034fe49f1789a NeedsCompilation: yes Package: qsea Version: 1.10.0 Depends: R (>= 3.5) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager License: GPL (>= 2) MD5sum: 0fae5fe514b3c766dd6df177706887a2 NeedsCompilation: yes Package: qsmooth Version: 1.0.0 Depends: R (>= 3.6.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: CC BY 4.0 MD5sum: d4e7613cae77fa6e53984260041a71d4 NeedsCompilation: no Package: QSutils Version: 1.2.0 Depends: R (>= 3.5), Biostrings, BiocGenerics,methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: file LICENSE MD5sum: 546493a7b9a5316616aa61281e3b4d36 NeedsCompilation: no Package: QUALIFIER Version: 1.28.0 Depends: R (>= 2.14.0),flowCore,flowViz,ncdfFlow,flowWorkspace, data.table,reshape Imports: MASS,hwriter,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,latticeExtra,grDevices,tools, Biobase,XML,grid Suggests: RSVGTipsDevice, knitr License: Artistic-2.0 MD5sum: 2c6692e2c10c358cc2caa8d0947c1620 NeedsCompilation: no Package: quantro Version: 1.18.0 Depends: R (>= 3.1.3) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: knitr, RUnit, BiocGenerics, BiocStyle License: GPL (>= 3) MD5sum: c271662d585e8997b71f103a08dacf8a NeedsCompilation: no Package: quantsmooth Version: 1.50.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: 06ba796cd1e44554ed3e62d234269d6b NeedsCompilation: no Package: QuartPAC Version: 1.16.0 Depends: iPAC, GraphPAC, SpacePAC, data.table Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: d47f56657de973251a31d1b66909329f NeedsCompilation: no Package: QuasR Version: 1.24.2 Depends: R (>= 3.6), parallel, GenomicRanges (>= 1.13.3), Rbowtie Imports: methods, grDevices, graphics, utils, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools (>= 1.99.1), GenomicFeatures (>= 1.17.13), ShortRead (>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi LinkingTo: Rhtslib (>= 1.15.3) Suggests: Gviz, BiocStyle, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: f85161c3210e2369117373dcd8e87902 NeedsCompilation: yes Package: QuaternaryProd Version: 1.18.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: 1123375c16ab1573f3885096bf438f22 NeedsCompilation: yes Package: QUBIC Version: 1.12.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 62cc1d219fac17e3d73e77ecbfb1dc10 NeedsCompilation: yes Package: qusage Version: 2.18.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans License: GPL (>= 2) MD5sum: 6ce81ce507c1b76c40a33058159813ee NeedsCompilation: no Package: qvalue Version: 2.16.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL MD5sum: 2606ad06ad8b41c16fa5b6cc7a9f14ba NeedsCompilation: no Package: R3CPET Version: 1.16.0 Depends: R (>= 3.2), Rcpp (>= 0.10.4), methods Imports: methods, parallel, clues, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), ggbio LinkingTo: Rcpp Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) MD5sum: 5d62ab7bf2c8e55bc2ed601855ce4d86 NeedsCompilation: yes Package: r3Cseq Version: 1.30.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 MD5sum: b39e873a2ae7044574684b964168f7e0 NeedsCompilation: no Package: R453Plus1Toolbox Version: 1.34.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: c13e0ea174443f8c59551b6797f15977 NeedsCompilation: yes Package: R4RNA Version: 1.12.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 MD5sum: 4ce7f63eb631f73c6cb99ce4ef43c5e7 NeedsCompilation: no Package: RaggedExperiment Version: 1.8.0 Depends: R (>= 3.5.0), GenomicRanges Imports: BiocGenerics, GenomeInfoDb, IRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, MultiAssayExperiment License: Artistic-2.0 MD5sum: 3fdea8716d8fde43aa363a97dafcd91f NeedsCompilation: no Package: rain Version: 1.18.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: 65a71f22d50df3704c7d697a2e78dbfd NeedsCompilation: no Package: rama Version: 1.58.0 Depends: R(>= 2.5.0) License: GPL (>= 2) MD5sum: 09183bff22ae8499d8f99175f334c193 NeedsCompilation: yes Package: ramwas Version: 1.8.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 1e3f7ddaa2171b7a1889ddb830d12712 NeedsCompilation: yes Package: RandomWalkRestartMH Version: 1.4.0 Depends: R(>= 3.5.0) Imports: igraph, Matrix, dnet, methods Suggests: BiocStyle, testthat License: GPL (>= 2) MD5sum: 969cdbf1c3cac6c81e8c7a0d47e8ba13 NeedsCompilation: no Package: randPack Version: 1.30.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: 063a95e021d78fe49fc130d47493c892 NeedsCompilation: no Package: RankProd Version: 3.10.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: 2df702820b143840f7a35de342f2aa92 NeedsCompilation: no Package: RareVariantVis Version: 2.12.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: 264c45546060173959e66bdce31ad53f NeedsCompilation: no Package: Rariant Version: 1.20.0 Depends: R (>= 3.0.2), GenomicRanges, VariantAnnotation Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr, reshape2 Suggests: h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 35bff83f4c34da31a2cbea4dfcfe2894 NeedsCompilation: no Package: RbcBook1 Version: 1.52.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: d27a11f7a88414446ebca92f66665b5b NeedsCompilation: no Package: RBGL Version: 1.60.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 300bba134b21fa85d6b24efa5a0ec21c NeedsCompilation: yes Package: RBioinf Version: 1.44.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 MD5sum: c157e29f804f8b12ec5771f2283f1850 NeedsCompilation: yes Package: rBiopaxParser Version: 2.24.0 Depends: R (>= 3.0.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL, igraph License: GPL (>= 2) MD5sum: b8e64e8bcf94e7674e7b5bcda29cd06c NeedsCompilation: no Package: RBM Version: 1.16.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) MD5sum: ef9b3a8bb641fc13f7d536400f49dd64 NeedsCompilation: no Package: Rbowtie Version: 1.24.0 Suggests: parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 MD5sum: 6b2e05e40fda2c1f4d5671167fca5bf5 NeedsCompilation: yes Package: Rbowtie2 Version: 1.6.0 Depends: R (>= 3.5) Suggests: knitr License: GPL (>= 3) Archs: x64 MD5sum: f77a146308dcd3517165fec88262caa7 NeedsCompilation: yes Package: rbsurv Version: 2.42.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) MD5sum: 9e7d74ec22e1d4b835daa9eaea04f65c NeedsCompilation: no Package: Rcade Version: 1.26.0 Depends: R (>= 2.14.0), methods, GenomicRanges, Rsamtools, baySeq Imports: utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors, IRanges, GenomeInfoDb, GenomicAlignments Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: fdd9ad4b78ffed906437541c24fd7d86 NeedsCompilation: no Package: RCAS Version: 1.10.1 Depends: R (>= 3.3.0), plotly (>= 4.5.2), DT (>= 0.2), data.table, topGO, motifRG Imports: biomaRt, AnnotationDbi, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, org.Hs.eg.db, GenomicFeatures, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, stats, plotrix, pbapply, RSQLite, proxy, DBI, pheatmap, ggplot2, cowplot, ggseqlogo, methods, utils Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10, BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db, org.Dm.eg.db, testthat, covr License: Artistic-2.0 MD5sum: 77dcdca0256d0efb9a29c3f26e14f21e NeedsCompilation: no Package: RCASPAR Version: 1.30.0 License: GPL (>= 3) MD5sum: 306067d091c8eb65e9a09bcef1a65b19 NeedsCompilation: no Package: rcellminer Version: 2.6.0 Depends: R (>= 3.2), Biobase, rcdk, fingerprint, rcellminerData Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW, parallel License: LGPL-3 + file LICENSE MD5sum: fabbb8cb40bd48d4722e3a31cdec57f5 NeedsCompilation: no Package: rCGH Version: 1.14.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 522541f1b2847440b4f8b4507db575be NeedsCompilation: no Package: Rchemcpp Version: 2.21.1 Depends: R (>= 2.15.0) Imports: Rcpp (>= 0.11.1), methods, ChemmineR LinkingTo: Rcpp Suggests: apcluster, kernlab License: GPL (>= 2.1) MD5sum: 7baa3710ac856f7b70b580e127f0aa0e NeedsCompilation: yes Package: RchyOptimyx Version: 2.24.0 Depends: R (>= 2.10) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices, flowType (>= 2.0.0) Suggests: flowCore License: Artistic-2.0 MD5sum: 31073dc97f960a5b01c81c383bbe40e6 NeedsCompilation: yes Package: RcisTarget Version: 1.4.0 Depends: R (>= 3.4) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, feather, graphics, GSEABase, methods, R.utils, stats, SummarizedExperiment, utils Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork Enhances: doMC, doRNG, zoo License: GPL-3 MD5sum: adc62e71ca1030c785f3c0e80a1a60c7 NeedsCompilation: no Package: RCM Version: 1.0.0 Imports: RColorBrewer, alabama, edgeR, reshape2, tseries, vegan, VGAM, ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS, stats, grDevices, graphics, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 8d34d630c361a2426ae5054ba7e536b1 NeedsCompilation: no Package: Rcpi Version: 1.20.1 Depends: R (>= 3.0.2) Imports: stats, utils, methods, RCurl, rjson, foreach, doParallel, Biostrings, GOSemSim, ChemmineR, fmcsR, rcdk (>= 3.3.8) Suggests: knitr, rmarkdown, RUnit, BiocGenerics Enhances: ChemmineOB License: Artistic-2.0 | file LICENSE MD5sum: b2b1cdba649c3638f98dd463e23366bb NeedsCompilation: no Package: Rcwl Version: 1.0.14 Depends: R (>= 3.6), yaml, methods, S4Vectors Imports: utils, stats, BiocParallel, batchtools, DiagrammeR, shiny, R.utils, codetools Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: aa0353fed4a9c5ea673ad0f873deb930 NeedsCompilation: no Package: RcwlPipelines Version: 1.0.11 Depends: R (>= 3.6), Rcwl, BiocFileCache Imports: dplyr, rappdirs, jsonlite, methods Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: c0ce21510faf5e38997b09af62e77703 NeedsCompilation: no Package: RCy3 Version: 2.4.6 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 85c7936fd19a6c71ac7094b421eb9a7c NeedsCompilation: no Package: RCyjs Version: 2.6.0 Depends: R (>= 3.5.0), BrowserViz (>= 2.5.14), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, RefNet, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b08a087c3857b27c5a97c92de29a2b98 NeedsCompilation: no Package: RDAVIDWebService Version: 1.22.0 Depends: R (>= 2.14.1), methods, graph, GOstats, ggplot2 Imports: Category, GO.db, RBGL, rJava Suggests: Rgraphviz License: GPL (>= 2) MD5sum: 3b8b125d8f39ee1f0b017168127a8661 NeedsCompilation: no Package: rDGIdb Version: 1.10.0 Imports: jsonlite,httr,methods,graphics Suggests: BiocStyle,knitr,testthat License: MIT + file LICENSE MD5sum: e8ea9465dfeff48d4475c8375f2bc2c4 NeedsCompilation: no Package: Rdisop Version: 1.44.0 Depends: R (>= 2.0.0), Rcpp LinkingTo: Rcpp Suggests: RUnit License: GPL-2 MD5sum: 13e4b81c9b0e526c06e97789f32f9a40 NeedsCompilation: yes Package: RDRToolbox Version: 1.34.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) MD5sum: 2b190cad4839dd6c06b6bca0cbe5996c NeedsCompilation: no Package: ReactomePA Version: 1.28.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph, reactome.db, igraph, graphite Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc, testthat License: GPL-2 MD5sum: 18193e4881138989bcd4333944982058 NeedsCompilation: no Package: readat Version: 1.10.0 Depends: R (>= 3.4.0) Imports: assertive.base (>= 0.0-7), assertive.files (>= 0.0-2), assertive.numbers (>= 0.0-2), assertive.properties (>= 0.0-4), assertive.sets (>= 0.0-3), assertive.types (>= 0.0-3), Biobase (>= 2.34.0), data.table (>= 1.10.4), dplyr (>= 0.5.0), magrittr (>= 1.5), openxlsx (>= 4.0.17), pathological (>= 0.1-2), reshape2 (>= 1.4.2), stats, stringi (>= 1.1.5), SummarizedExperiment (>= 1.4.0), testthat (>= 1.0.2), tidyr (>= 0.6.2), utils Suggests: knitr, MSnbase, rmarkdown, withr License: GPL-3 MD5sum: 8507f3bf56c2e3ac48cbe25e364a9c45 NeedsCompilation: no Package: ReadqPCR Version: 1.30.0 Depends: R(>= 2.14.0), Biobase, methods Suggests: qpcR License: LGPL-3 MD5sum: 086211aa45bcbff6dcfde3efe7bd781c NeedsCompilation: no Package: reb Version: 1.62.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 MD5sum: 207f4057530bd1b3ced23270a7a11925 NeedsCompilation: yes Package: REBET Version: 1.2.0 Depends: ASSET Imports: stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 776e872bca2020d7cc861bfc798478b0 NeedsCompilation: yes Package: recount Version: 1.10.13 Depends: R (>= 3.3.0), SummarizedExperiment Imports: BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer (>= 1.35.3), S4Vectors, stats, utils Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: de9885a00e3a64c040e8dae7b7de00e3 NeedsCompilation: no Package: recoup Version: 1.12.0 Depends: R (>= 2.13.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, circlize, graphics, grDevices, methods, rtracklayer, plyr, stats, utils Suggests: grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RSQLite, RMySQL Enhances: parallel License: GPL (>= 3) MD5sum: 3aae87e834e6ba51e39a16426611a8fc NeedsCompilation: no Package: RedeR Version: 1.32.2 Depends: R (>= 3.3.3), methods Imports: igraph Suggests: pvclust, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: cacdfd5d103b4c5616aab1e0c92cc116 NeedsCompilation: no Package: REDseq Version: 1.30.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges (>= 1.13.5), multtest, stats, utils License: GPL (>= 2) MD5sum: 28992addf8f0a83b68e7a3188cd5f442 NeedsCompilation: no Package: RefNet Version: 1.20.0 Depends: R (>= 2.15.0), methods, IRanges, PSICQUIC, AnnotationHub, RCurl, shiny Imports: BiocGenerics Suggests: RUnit, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: fef9148fdfb0828b0d06d6e6ec1d210a NeedsCompilation: no Package: RefPlus Version: 1.54.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) MD5sum: d56a965cd314a7cb995c993c6512a6c3 NeedsCompilation: no Package: regioneR Version: 1.16.5 Depends: GenomicRanges Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 MD5sum: 2e23d99b1e4fa5b1d9bafddbcfedb92a NeedsCompilation: no Package: regionReport Version: 1.18.2 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.1.0), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio (>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 MD5sum: 57c600cab25e846afa839c1d4a8bd7dd NeedsCompilation: no Package: regsplice Version: 1.10.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 32b236f311812f449bd9bd81b0a2bd3c NeedsCompilation: no Package: REMP Version: 1.8.2 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 2c0e55ea370a09491d2592d6be48679a NeedsCompilation: no Package: Repitools Version: 1.30.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: be4217174c229d982e547851342de8d8 NeedsCompilation: yes Package: ReportingTools Version: 2.24.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 10cc6f059f95b306df1b1e3ddd7a788d NeedsCompilation: no Package: RepViz Version: 1.0.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: knitr, testthat License: GPL-3 MD5sum: d0c0a511327feb084f01ac4c22b56ae7 NeedsCompilation: no Package: ReQON Version: 1.30.0 Depends: R (>= 3.0.2), Rsamtools, seqbias Imports: rJava, graphics, stats, utils, grDevices Suggests: BiocStyle License: GPL-2 MD5sum: 3d26cf04e111979ca2b1e349c4256720 NeedsCompilation: no Package: restfulSE Version: 1.6.1 Depends: R (>= 3.6), SummarizedExperiment,DelayedArray Imports: utils, stats, methods, S4Vectors, Biobase,reshape2, AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1), magrittr, bigrquery, ExperimentHub, AnnotationHub, rlang Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle, restfulSEData License: Artistic-2.0 MD5sum: 0a3a3e0aedcb62b296c81e4a2250030b NeedsCompilation: no Package: rexposome Version: 1.6.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 6aa1e97a833510086fea68191f1f8c68 NeedsCompilation: no Package: rfPred Version: 1.22.0 Depends: Rsamtools, GenomicRanges, IRanges, data.table, methods, parallel Suggests: BiocStyle License: GPL (>= 2) MD5sum: 42a8359f2e811af6d85b9944b07b6d26 NeedsCompilation: yes Package: rGADEM Version: 2.32.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, IRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: e74557572cacc6c9fee8f5112fdf3df6 NeedsCompilation: yes Package: RGalaxy Version: 1.28.0 Depends: XML, methods, tools, optparse Imports: BiocGenerics, Biobase, roxygen2 Suggests: RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve Enhances: RSclient License: Artistic-2.0 MD5sum: f6f4addc405440ff80b290bdbacfb468 NeedsCompilation: no Package: Rgin Version: 1.4.0 Depends: R (>= 3.5) LinkingTo: RcppEigen (>= 0.3.3.5.0) Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: f67682923c47b4b278d728cf815f8a44 NeedsCompilation: yes Package: RGMQL Version: 1.4.1 Depends: R(>= 3.4.2), RGMQLlib Imports: httr, rJava, GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, methods, S4Vectors, dplyr, stats, glue, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 4d66a93139d143dadf4eeb716df01b58 NeedsCompilation: no Package: RGraph2js Version: 1.12.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: fd88db04ecb5dbe766ee4e2d4bdac794 NeedsCompilation: no Package: Rgraphviz Version: 2.28.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: 939f3939e3bed3a546143ed40f95e722 NeedsCompilation: yes Package: rGREAT Version: 1.16.1 Depends: R (>= 3.1.2), GenomicRanges, IRanges, methods Imports: rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats Suggests: testthat (>= 0.3), knitr, circlize (>= 0.4.8), rmarkdown License: MIT + file LICENSE MD5sum: 8ecee45e6702d3c6143c673360a6bca1 NeedsCompilation: no Package: RGSEA Version: 1.18.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: e981c0f0c51104ee88b7ac9c89154ad6 NeedsCompilation: no Package: rgsepd Version: 1.16.0 Depends: R (>= 3.5.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, hash, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: f42efca6296232068359728818cd0365 NeedsCompilation: no Package: rhdf5 Version: 2.28.1 Depends: R (>= 3.5.0), methods Imports: Rhdf5lib (>= 1.3.2) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2 License: Artistic-2.0 MD5sum: d39c11bfeee4b4f1dcb1c6c0364ab7e4 NeedsCompilation: yes Package: rhdf5client Version: 1.6.1 Depends: R (>= 3.5), methods, DelayedArray Imports: S4Vectors, httr, R6, rjson, utils Suggests: knitr, testthat, BiocStyle, DT, reticulate License: Artistic-2.0 MD5sum: 47721d9b1cda750b431fdbd5192bffb7 NeedsCompilation: yes Package: Rhdf5lib Version: 1.6.3 Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1257d1377dcd9916065d485de4dd0f9c NeedsCompilation: yes Package: Rhisat2 Version: 1.0.3 Depends: R (>= 3.6) Imports: GenomicFeatures, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: f9d31bd584dfe3437fa23e13ad57bf8e NeedsCompilation: yes Package: Rhtslib Version: 1.16.3 Imports: zlibbioc LinkingTo: zlibbioc Suggests: BiocStyle, knitr License: LGPL (>= 2) MD5sum: 282f0711596d1f25f4221b791046459e NeedsCompilation: yes Package: rHVDM Version: 1.49.0 Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 30ac36983f2746d0d2ee2be4ee6ba55d NeedsCompilation: no Package: RiboProfiling Version: 1.14.0 Depends: R (>= 3.2.2), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 30da7540d39e7c752c224c226322f6df NeedsCompilation: no Package: riboSeqR Version: 1.18.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 4e9c3e5e2eac839d8fc9fac1bac3b5b7 NeedsCompilation: no Package: RImmPort Version: 1.12.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 74e9aacd1917e4ea6b968bd30371db56 NeedsCompilation: no Package: Ringo Version: 1.48.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 MD5sum: 905cfe4b4a6f9bf4bcfbdf0250c7cc0c NeedsCompilation: yes Package: RIPSeeker Version: 1.24.0 Depends: R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures License: GPL-2 MD5sum: f2b707b4fca1df7b241ef4b24a85fcb6 NeedsCompilation: no Package: Risa Version: 1.26.0 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL MD5sum: cae993c23c4cf66321261b1115a18500 NeedsCompilation: no Package: RITAN Version: 1.8.0 Depends: R (>= 3.4), Imports: graphics, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, sqldf, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata Suggests: rmarkdown License: file LICENSE MD5sum: d9be8da5c38acb02332534452faf630c NeedsCompilation: no Package: RIVER Version: 1.8.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: 87b2517810b6bdad09d5cb027946a3fe NeedsCompilation: no Package: RJMCMCNucleosomes Version: 1.8.0 Depends: R (>= 3.4), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors, BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 855eb918b7b4c78face174a2b7f4ede2 NeedsCompilation: yes Package: RLMM Version: 1.46.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: a3796e7da8e9a0dc62085026207c22ca NeedsCompilation: no Package: Rmagpie Version: 1.40.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 42d34c1f3fa1f5390b12488fe0c3da9a NeedsCompilation: no Package: RMassBank Version: 2.12.0 Depends: Rcpp Imports: XML,RCurl,rjson,S4Vectors,digest, rcdk,yaml,mzR,methods,Biobase,MSnbase,httr Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, RUnit, enviPat License: Artistic-2.0 MD5sum: 9cadbd9a88b737eed282e0563f918b64 NeedsCompilation: no Package: rMAT Version: 3.33.0 Depends: R(>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), Biobase (>= 2.15.1), affxparser Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4 Suggests: GenomeGraphs, rtracklayer License: Artistic-2.0 MD5sum: 707db595db889f056a62d5802dc0e291 NeedsCompilation: yes Package: rmelting Version: 1.0.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.5-0) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: 169898a7e014553431e1adf202502a20 NeedsCompilation: no Package: RmiR Version: 1.40.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 MD5sum: 648f2070b121489b7d478d80cfe774a0 NeedsCompilation: no Package: Rmmquant Version: 1.2.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 050e95348776d7b8b0b5bdfb08715b21 NeedsCompilation: yes Package: RNAdecay Version: 1.4.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 7fe84f6a5edb236cf8dcd1a88f649155 NeedsCompilation: yes Package: RNAinteract Version: 1.32.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 MD5sum: edc219a8b4c1af4ee194087c5e34bacf NeedsCompilation: no Package: RNAither Version: 2.32.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 MD5sum: 49c001354fe14669a8996adbd56f79ee NeedsCompilation: no Package: RNAprobR Version: 1.16.0 Depends: R (>= 3.1.1), GenomicFeatures(>= 1.16.3), plyr(>= 1.8.1), BiocGenerics(>= 0.10.0) Imports: Biostrings(>= 2.32.1), GenomicRanges(>= 1.16.4), IRanges(>= 2.10.5), Rsamtools(>= 1.16.1), rtracklayer(>= 1.24.2), GenomicAlignments(>= 1.5.12), S4Vectors(>= 0.14.7), graphics, stats, utils Suggests: BiocStyle License: GPL (>= 2) MD5sum: 4fd50c68767817514dfd3f24012ee68a NeedsCompilation: no Package: rnaseqcomp Version: 1.14.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 070446c7cfa966892b854ce6fdc4b6ab NeedsCompilation: no Package: rnaSeqMap Version: 2.42.0 Depends: R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments Imports: GenomicRanges , IRanges, edgeR, DESeq, DBI License: GPL-2 MD5sum: 3534ea405fc475ddc1e002f7918f20f3 NeedsCompilation: yes Package: RNASeqPower Version: 1.24.0 License: LGPL (>= 2) MD5sum: 128398a48bdc1d1cb763643a72e4725d NeedsCompilation: no Package: RNASeqR Version: 1.2.1 Depends: R(>= 3.5.0), ggplot2, pathview, edgeR, methods Imports: Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib, FactoMineR, factoextra, corrplot, PerformanceAnalytics, reshape2, DESeq2, systemPipeR, systemPipeRdata, clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr, pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings, parallel Suggests: knitr, png, grid, RNASeqRData License: Artistic-2.0 MD5sum: f22237e57f8ee4dd44d961f5a8b55f2f NeedsCompilation: no Package: RnaSeqSampleSize Version: 1.16.0 Depends: R (>= 2.10), RnaSeqSampleSizeData Imports: biomaRt,edgeR,heatmap3,matlab,KEGGREST,Rcpp (>= 0.11.2) LinkingTo: Rcpp Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 58a066d152246ca13c8436c1be1a17d9 NeedsCompilation: yes Package: RnBeads Version: 2.2.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit License: GPL-3 MD5sum: bbf902d71dbc1ff3140b69786eec53a8 NeedsCompilation: no Package: Rnits Version: 1.18.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: f2dc9da60be5b567aa10ee868f420f76 NeedsCompilation: no Package: roar Version: 1.20.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: 92ef146820e62dc15b03d47103b7b842 NeedsCompilation: no Package: ROC Version: 1.60.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 MD5sum: e8b0381abdb97b4e05462c5aa9cb1b40 NeedsCompilation: yes Package: Roleswitch Version: 1.22.0 Depends: R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI Suggests: ggplot2 License: GPL-2 MD5sum: e5b8341739aaa57153f976065382980c NeedsCompilation: no Package: rols Version: 2.12.2 Depends: methods Imports: httr, progress, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 MD5sum: 0a00e23d4f5f2cbfc84506e229c857c1 NeedsCompilation: no Package: ROntoTools Version: 2.12.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: fbd173389451d2dba4d9cab0d6d0aa43 NeedsCompilation: no Package: ropls Version: 1.16.0 Depends: Biobase Imports: graphics, grDevices, methods, stats Suggests: BiocGenerics, BiocStyle, knitr, multtest, rmarkdown, testthat License: CeCILL MD5sum: 6f400551a42309cdab9516e3a3699310 NeedsCompilation: no Package: ROTS Version: 1.12.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 855cd21624ca96a2d869308321c15455 NeedsCompilation: yes Package: RPA Version: 1.40.0 Depends: R (>= 3.1.1), affy, BiocGenerics, methods Imports: phyloseq Suggests: affydata, knitr, parallel License: BSD_2_clause + file LICENSE MD5sum: cdf4f68b4db2f44027ab8a2b64cd6fbc NeedsCompilation: no Package: RProtoBufLib Version: 1.6.0 License: BSD_3_clause MD5sum: 051dff736a8a9472967af4ab7592eb75 NeedsCompilation: yes Package: RpsiXML Version: 2.26.0 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI License: LGPL-3 MD5sum: d1e54d5af83439601aa072ed9cd9813a NeedsCompilation: no Package: rpx Version: 1.20.2 Depends: methods Imports: xml2, RCurl, utils Suggests: MSnbase, Biostrings, BiocStyle, testthat, knitr License: GPL-2 MD5sum: 1c4e7c49c608fb031a02fb1884f77360 NeedsCompilation: no Package: Rqc Version: 1.18.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 8179a6fd97cb7e253b3e9b0b4930213c NeedsCompilation: yes Package: rqt Version: 1.10.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: be2f07e3861cacc72175b7211849ba08 NeedsCompilation: no Package: rqubic Version: 1.30.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: d76444400bdf99e353f4ff3ef6ce3597 NeedsCompilation: yes Package: rRDP Version: 1.18.0 Depends: Biostrings (>= 2.26.2) Suggests: rRDPData License: GPL-2 | file LICENSE MD5sum: 943c2acf0f62f3132d9e6a3f4c0301e5 NeedsCompilation: no Package: RRHO Version: 1.24.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: 7da61e5969e445ef71938c8e1f627276 NeedsCompilation: no Package: Rsamtools Version: 2.0.3 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel LinkingTo: Rhtslib (>= 1.16.3), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 476ab63bc7b1f137864f3b9daecae961 NeedsCompilation: yes Package: rsbml Version: 2.42.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: 8a1462618926a032d37ad539386304bf NeedsCompilation: yes Package: rScudo Version: 1.0.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 12e0c91e5d423a7ec438ac459ded02b3 NeedsCompilation: no Package: RSeqAn Version: 1.4.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: a758f8f9fd49a40baab1a0e875a0b33f NeedsCompilation: yes Package: rSFFreader Version: 0.31.0 Depends: ShortRead (>= 1.23.17) Imports: methods, Biostrings, IRanges LinkingTo: S4Vectors (>= 0.13.8), IRanges, XVector, Biostrings Suggests: xtable License: Artistic-2.0 MD5sum: 3358439570e653a0993554a493c46025 NeedsCompilation: yes Package: Rsubread Version: 1.34.7 Imports: grDevices, stats, utils License: GPL-3 MD5sum: 9351f249c26db468b738bd3421d241de NeedsCompilation: yes Package: RSVSim Version: 1.24.0 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 MD5sum: 6e49fea17a802712a961c19759ad5426 NeedsCompilation: no Package: rTANDEM Version: 1.24.0 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: methods LinkingTo: Rcpp Suggests: biomaRt License: Artistic-1.0 | file LICENSE MD5sum: 44208a1e3fa4519631026eaaca1c6f06 NeedsCompilation: yes Package: RTCA Version: 1.36.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: fd9e6aa7833069a60b2bfeddf8071d19 NeedsCompilation: no Package: RTCGA Version: 1.14.0 Depends: R (>= 3.3.0) Imports: XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr License: GPL-2 MD5sum: 197a319790d242d89d7c2a70eec3f209 NeedsCompilation: no Package: RTCGAToolbox Version: 2.14.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, IRanges, limma, methods, RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors, stringr, SummarizedExperiment, survival, TCGAutils, XML Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: file LICENSE MD5sum: 012e8a4cbfb4a00a4828f81d516adf97 NeedsCompilation: no Package: RTN Version: 2.8.5 Depends: R (>= 3.5.0), methods Imports: RedeR, minet, viper, mixtools, snow, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8fd3636a2953f28b61d770604e273146 NeedsCompilation: no Package: RTNduals Version: 1.8.3 Depends: R(>= 3.5), RTN(>= 2.6.3), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e5f7c7d0e1862849648c1169ce4d4b73 NeedsCompilation: no Package: RTNsurvival Version: 1.8.3 Depends: R(>= 3.5), RTN(>= 2.6.3), RTNduals(>= 1.6.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: cda5cee139112bd398b2b9a8bd29aaba NeedsCompilation: no Package: RTopper Version: 1.30.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) MD5sum: e1c2eb8d873ba6524793846bae561bca NeedsCompilation: no Package: rtracklayer Version: 1.44.4 Depends: R (>= 3.3), methods, GenomicRanges (>= 1.31.8) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.19.22), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: cbe4719c18316f234282afcd700e7921 NeedsCompilation: yes Package: Rtreemix Version: 1.46.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: 8fd53d3b038779d64d0c79e458073794 NeedsCompilation: yes Package: rTRM Version: 1.22.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 License: GPL-3 MD5sum: e58e2df0a7aa36fef947ec613787e6ff NeedsCompilation: no Package: rTRMui Version: 1.22.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: b68c48722a81e8e7538326a8d620bdb0 NeedsCompilation: no Package: runibic Version: 1.6.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE MD5sum: c8f01e6c053657c2965534977c011fd3 NeedsCompilation: yes Package: RUVcorr Version: 1.16.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2 Suggests: knitr, BiocStyle, hgu133a2.db License: GPL-2 MD5sum: f6531125e9cdbe8b059809cca024282f NeedsCompilation: no Package: RUVnormalize Version: 1.18.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 6dbb367a168bc1afdd02500678511afe NeedsCompilation: no Package: RUVSeq Version: 1.18.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: bacf3b82eb0dfaf71deedde3f134197e NeedsCompilation: no Package: RVS Version: 1.6.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: f291c45d810295d1c0807c8c15b04fab NeedsCompilation: no Package: rWikiPathways Version: 1.4.1 Imports: caTools, httr, RJSONIO, utils, XML Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 912bba22fad85590052d44ae6b7cb76e NeedsCompilation: no Package: S4Vectors Version: 0.22.1 Depends: R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>= 0.23.3) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 477716e7ece4e3dea37cff1375d305ad NeedsCompilation: yes Package: safe Version: 3.24.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 25aa7f520ac63c8278502724744081a5 NeedsCompilation: no Package: sagenhaft Version: 1.54.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) MD5sum: c7bc38a2be0fbefcaa1574b9eabc4e37 NeedsCompilation: no Package: SAGx Version: 1.58.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 MD5sum: 492ec5dae06e1ee6efd1727720220d18 NeedsCompilation: yes Package: samExploreR Version: 1.8.0 Depends: ggplot2,Rsubread,RNAseqData.HNRNPC.bam.chr14,edgeR,R (>= 3.4.0) Imports: grDevices, stats, graphics Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL-3 MD5sum: b474822f7c070af3860e1d6099963b91 NeedsCompilation: no Package: sampleClassifier Version: 1.8.0 Depends: R (>= 3.4), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 62a530a8913a194cd3d1ef7f597c0c30 NeedsCompilation: no Package: SamSPECTRAL Version: 1.38.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 57b8e4af80ec16503f640076e448df6a NeedsCompilation: yes Package: sangerseqR Version: 1.20.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 31264d633b121298f642ed7e79e366d1 NeedsCompilation: no Package: SANTA Version: 2.22.0 Depends: R (>= 2.14), igraph Imports: Matrix, snow Suggests: RUnit, BiocGenerics, knitr, knitcitations, formatR, org.Sc.sgd.db, BioNet, DLBCL, msm License: GPL (>= 2) MD5sum: 6ba9ce317557ad49c1147be11dc9024b NeedsCompilation: yes Package: sapFinder Version: 1.22.0 Depends: R (>= 3.0.0),rTANDEM (>= 1.3.5) Imports: pheatmap,Rcpp (>= 0.10.6),graphics,grDevices,stats, utils LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: 6d6a661040edbe9d0adb12390988e71e NeedsCompilation: yes Package: savR Version: 1.22.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo, testthat License: AGPL-3 MD5sum: 7baac100f53958464842eb9cd31d4759 NeedsCompilation: no Package: SBMLR Version: 1.80.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: ff571f4e83243d39124016025836e7a3 NeedsCompilation: no Package: SC3 Version: 1.12.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater License: GPL-3 MD5sum: 198efa24f98a1c941fa8ad793d582e12 NeedsCompilation: yes Package: Scale4C Version: 1.6.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 12361c8ea9c3d72f3560fac83015a116 NeedsCompilation: no Package: scAlign Version: 1.0.0 Depends: R (>= 3.5) Imports: SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 08d737df935ad85a6b65cba882bf18f5 NeedsCompilation: no Package: SCAN.UPC Version: 2.26.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 60fdbafce89a0c2eea88316bab3d2f4b NeedsCompilation: no Package: scater Version: 1.12.2 Depends: R (>= 3.6), SingleCellExperiment, ggplot2 Imports: BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel LinkingTo: Rcpp, beachmat Suggests: BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma License: GPL-3 MD5sum: 851f38f58e1f9b1e1f6112d273d5ddbe NeedsCompilation: yes Package: SCBN Version: 1.2.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 MD5sum: 70393c9f4b1630bf8d79e103c06bc43c NeedsCompilation: no Package: scDD Version: 1.8.0 Depends: R (>= 3.4) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 68b1fb9761657eb28f9b90e796d2e92b NeedsCompilation: yes Package: scde Version: 2.12.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 1bc7fdc7e95e1fe2c34684111e503668 NeedsCompilation: yes Package: scds Version: 1.0.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot License: MIT + file LICENSE MD5sum: 3cbb33a493bb7e80601d4517d097571f NeedsCompilation: no Package: scFeatureFilter Version: 1.4.0 Depends: R (>= 3.5) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 24ca2e4e62ed8d14aac28b73efe1c449 NeedsCompilation: no Package: scfind Version: 1.6.0 Depends: R(>= 3.4) Imports: SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: e258b0f73b91921b7c068431b09fa3db NeedsCompilation: yes Package: ScISI Version: 1.56.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL MD5sum: 08db1fc90b15828040a6c7a997052f24 NeedsCompilation: no Package: scmap Version: 1.6.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: fbfc24aaeecf65952e59e18f2c598db7 NeedsCompilation: yes Package: scMerge Version: 1.0.0 Depends: R (>= 3.6.0) Imports: BiocParallel, cluster, distr, doSNOW, foreach, igraph, irlba, iterators, matrixStats, M3Drop (>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, rsvd, S4Vectors, SingleCellExperiment, SummarizedExperiment LinkingTo: Rcpp (>= 0.12.18), RcppEigen, testthat Suggests: BiocStyle, covr, knitr, Matrix, rmarkdown, scales, scater, testthat License: GPL-3 MD5sum: 38fc29f95339fe69c968234be33ac4ee NeedsCompilation: yes Package: scmeth Version: 1.4.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: 3842b6dbd7a08a3f2e2d780ac1278cdd NeedsCompilation: no Package: SCnorm Version: 1.6.0 Depends: R (>= 3.4.0), Imports: stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, SingleCellExperiment, SummarizedExperiment, S4Vectors, ggplot2, forcats Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 03654c349ec319e48ba68c201858730e NeedsCompilation: no Package: scone Version: 1.8.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork License: Artistic-2.0 MD5sum: 0320a55f3d8bfedec227455ea94625e8 NeedsCompilation: no Package: Sconify Version: 1.4.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e47d764c109c9805e7353c11958afe6e NeedsCompilation: no Package: scoreInvHap Version: 1.6.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: a2613081ec201c27e63afac172d80fa9 NeedsCompilation: no Package: scPipe Version: 1.6.0 Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr, GenomicRanges, magrittr, glue LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 7b3a3482d6610048fcdc9156f44610dd NeedsCompilation: yes Package: scran Version: 1.12.1 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp (>= 0.12.14), stats, methods, utils, Matrix, scater, edgeR, limma, dynamicTreeCut, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light License: GPL-3 MD5sum: 47c6eecbb45043814ee27edbb48be092 NeedsCompilation: yes Package: scRecover Version: 1.0.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>= 1.3.0), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 8cbf4391ae6493e1a8cfd34f7f585592 NeedsCompilation: no Package: scruff Version: 1.2.5 Depends: R (>= 3.5.0) Imports: data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, Rsubread, testthat License: MIT + file LICENSE MD5sum: 0e180f64a383d27cbf04d52992699624 NeedsCompilation: no Package: scsR Version: 1.20.0 Depends: R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings, IRanges, plyr, tcltk Imports: sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer Suggests: RUnit License: GPL-2 MD5sum: b6aa1d18d3ba19c7cf6b77052a550aad NeedsCompilation: no Package: scTensor Version: 1.0.13 Depends: R (>= 3.5.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork Suggests: testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens License: Artistic-2.0 MD5sum: f0cb261cc2efbf87d4f30b07070963e2 NeedsCompilation: no Package: SDAMS Version: 1.4.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 5d90e928e0187ec8d9f8f3a0013302f1 NeedsCompilation: no Package: segmentSeq Version: 2.18.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: f02009d37d365688285d7ca6106e7d27 NeedsCompilation: no Package: SELEX Version: 1.16.0 Depends: R (>= 2.7.0), rJava (>= 0.5-0), Biostrings (>= 2.26.0) License: GPL (>= 2) MD5sum: 94bd0e2afdff212e8f350f096e67b3c8 NeedsCompilation: no Package: SemDist Version: 1.18.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 9a7024a94ff4b88d11879bce11a2aaf3 NeedsCompilation: no Package: semisup Version: 1.8.0 Depends: R (>= 3.5.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 57a8dfe6011f2f46f1ca0960bd4309e7 NeedsCompilation: no Package: SEPA Version: 1.13.0 Depends: R(>= 2.10.0) Imports: ggplot2, shiny, topGO, segmented, reshape2, org.Hs.eg.db, org.Mm.eg.db Suggests: knitr License: GPL (>= 2) MD5sum: ad3202957761df88df45c4485fa1bfe8 NeedsCompilation: no Package: SEPIRA Version: 1.4.1 Depends: R (>= 3.5.0) Imports: limma (>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats Suggests: knitr, rmarkdown, testthat, igraph License: GPL-3 MD5sum: 5be9f7efd63a01f6b0d29a743a7b6ab4 NeedsCompilation: no Package: seq2pathway Version: 1.16.0 Depends: R (>= 2.10.0) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 37e014a88787011d7643a594a538b159 NeedsCompilation: no Package: SeqArray Version: 1.24.2 Depends: R (>= 3.5.0), gdsfmt (>= 1.18.0) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: ad853ee096353334f3870d7a7e38d510 NeedsCompilation: yes Package: seqbias Version: 1.32.0 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rhtslib (>= 1.15.3) Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: c4c6f16f1dffca33016753a4ed70d8b3 NeedsCompilation: yes Package: seqCAT Version: 1.6.3 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), lazyeval (>= 0.2.0), methods, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: befdb07b75f24653ebc5311faefa6492 NeedsCompilation: no Package: seqCNA Version: 1.30.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 4940c184d6dea7e54e8f31a025d39034 NeedsCompilation: yes Package: seqcombo Version: 1.6.0 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests: emojifont, knitr, prettydoc, tibble License: Artistic-2.0 MD5sum: ebf450a509b8bbd98589d6103a2b038b NeedsCompilation: no Package: SeqGSEA Version: 1.24.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 99baf889467af15810cf88111873c40f NeedsCompilation: no Package: seqLogo Version: 1.50.0 Depends: methods, grid Imports: stats4 License: LGPL (>= 2) MD5sum: 7d245f94e0c48b23022ad3b692187cb7 NeedsCompilation: no Package: seqPattern Version: 1.16.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 44e22955071d0a0964000501a064f5ee NeedsCompilation: no Package: seqplots Version: 1.22.2 Depends: R (>= 3.2.0) Imports: methods, IRanges, BSgenome, digest, rtracklayer, GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite, plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class, S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>= 0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: 69ef1cddcbe0454e1daa3cfaeae6491d NeedsCompilation: no Package: seqsetvis Version: 1.4.1 Depends: R (>= 3.5), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 69f63fef5fe3ba1253a1bfe4db346ecc NeedsCompilation: no Package: SeqSQC Version: 1.6.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 612ddfb4d761b1e6cd4cce005f087c1a NeedsCompilation: no Package: seqTools Version: 1.18.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 904b4952c0d23d19c87d8602bceeb870 NeedsCompilation: yes Package: SeqVarTools Version: 1.22.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, rlang, tidyr Suggests: BiocGenerics, BiocStyle, RUnit, stringr License: GPL-3 MD5sum: 59346cf539f2ccb4f4a793895400071c NeedsCompilation: no Package: sesame Version: 1.2.0 Depends: R (>= 3.5), sesameData, methods Imports: BiocParallel, R6, grDevices, utils, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors, randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle License: Artistic-2.0 MD5sum: c9e4ba0dc614dc3c0f55849a40b2535d NeedsCompilation: no Package: sevenbridges Version: 1.14.1 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, dplyr Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: efcacb4f31d0e0698fa3aae9266adf48 NeedsCompilation: no Package: sevenC Version: 1.4.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: 81ac097106bad8243943bcca8cc969c7 NeedsCompilation: no Package: SGSeq Version: 1.18.0 Depends: IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics, Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.17.28), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: d9a682543d590316afbaacd1391433cf NeedsCompilation: no Package: shinyMethyl Version: 1.20.0 Depends: methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>= 1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R (>= 3.0.0) Imports: RColorBrewer Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr License: Artistic-2.0 MD5sum: 4ce2a8ab4a4cd25c1d9d222ff8aa4147 NeedsCompilation: no Package: shinyTANDEM Version: 1.22.0 Depends: rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable License: GPL-3 MD5sum: 9d5e6eaa09ab0512d77bcb5c0821d759 NeedsCompilation: no Package: ShortRead Version: 1.42.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 MD5sum: 2acf79d7db1b63a807cc4a3e597b80bc NeedsCompilation: yes Package: SIAMCAT Version: 1.4.0 Depends: R (>= 3.5.0), mlr, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 2966081b0a9da9d2182c528d48b5f065 NeedsCompilation: no Package: SICtools Version: 1.14.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: a83288a7b568a23fb4e341d02898c93f NeedsCompilation: yes Package: sigaR Version: 1.32.0 Depends: Biobase, CGHbase, methods, mvtnorm, Imports: corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS, penalized, quadprog, snowfall, stats Suggests: CGHcall License: GPL (>= 2) MD5sum: 593f28de781124788a38acc25e3e95ea NeedsCompilation: no Package: SigCheck Version: 2.16.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: c976fbe0fc31ae7bfdbee833ba2a1af8 NeedsCompilation: no Package: sigFeature Version: 1.2.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr License: GPL MD5sum: 8fdee0fdd11816dea036a8bcc43f714b NeedsCompilation: no Package: SigFuge Version: 1.22.0 Depends: R (>= 3.1.1), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 630ba0ad1edb05c6c3f19b8d612e8163 NeedsCompilation: no Package: siggenes Version: 1.58.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: c94454bf57390fbc699c3b02144177d6 NeedsCompilation: no Package: sights Version: 1.10.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 114674c0f24aeacc971a581bb3f50cd3 NeedsCompilation: no Package: signeR Version: 1.10.0 Depends: VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, graphics, grDevices, GenomicRanges, nloptr, methods, stats, utils, PMCMR LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: eb18254515946efe1641254d1e3bd639 NeedsCompilation: yes Package: signet Version: 1.4.0 Depends: R (>= 3.4.0) Imports: graph, igraph, RBGL, graphics, utils, stats, methods Suggests: graphite, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: e1799bca498f155881e1eadfc9934cd5 NeedsCompilation: no Package: sigPathway Version: 1.52.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: e6b44d4bb6be64e4b25ac5a1682aa9f2 NeedsCompilation: yes Package: sigsquared Version: 1.16.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: c2a6ab23b6c6df437e2164bd22741a06 NeedsCompilation: no Package: SIM Version: 1.54.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 889785353c57a16d34e19c3c62652cea NeedsCompilation: yes Package: SIMAT Version: 1.16.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 205568831e77d3ad2c948c59897a98ac NeedsCompilation: no Package: SimBindProfiles Version: 1.22.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 MD5sum: a8a894ca754170d902be58c782e9644b NeedsCompilation: no Package: SIMD Version: 1.2.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: f16d1032aca332c206c4f96d1eb967cf NeedsCompilation: yes Package: similaRpeak Version: 1.16.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: cbe863e05270e59cb80abd239fbd1182 NeedsCompilation: no Package: SIMLR Version: 1.10.0 Depends: R (>= 3.6), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: e4b3f7ebe8ef92491f009efc463ccd2c NeedsCompilation: yes Package: simpleaffy Version: 2.60.0 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) MD5sum: cdc3ec6c91a8a9495b4bf5af62a5b1c8 NeedsCompilation: yes Package: simulatorZ Version: 1.18.0 Depends: R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost, BiocGenerics Imports: graphics, stats, gbm, Hmisc, GenomicRanges, methods Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc License: Artistic-2.0 MD5sum: c4e86e7faa46af6795bc943eb311384e NeedsCompilation: yes Package: sincell Version: 1.16.1 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 8d125ecd359a6cc8f4c29a647e3b92ca NeedsCompilation: yes Package: SingleCellExperiment Version: 1.6.0 Depends: SummarizedExperiment Imports: S4Vectors, methods, BiocGenerics, utils, stats Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne, Matrix License: GPL-3 MD5sum: e100bdfc9835d03ae02111994ec5e4d4 NeedsCompilation: no Package: singleCellTK Version: 1.4.2 Depends: R (>= 3.5), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, colourpicker, cluster, ComplexHeatmap, data.table, DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly, RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, shinycssloaders, shinythemes, umap Suggests: testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase, lintr License: MIT + file LICENSE MD5sum: f5633c1fa5af6778442173b84957817c NeedsCompilation: no Package: singscore Version: 1.4.0 Depends: R (>= 3.5),GSEABase Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 22d04aef20157eb31727850d14d61ef8 NeedsCompilation: no Package: SISPA Version: 1.14.0 Depends: R (>= 3.2),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: 9055444742c1fce2978063c887f3b2d1 NeedsCompilation: no Package: sitePath Version: 1.0.3 Depends: R (>= 3.6.0) Imports: ape, seqinr, Rcpp, methods, graphics, utils, stats LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: c78c94ab2b7d335de4323bb647f14bf4 NeedsCompilation: yes Package: sizepower Version: 1.54.0 Depends: stats License: LGPL MD5sum: aa63d5cfb52739ea3c771254418d12a9 NeedsCompilation: no Package: skewr Version: 1.16.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 0e217f39aa6dbe285584453fa6e5e710 NeedsCompilation: no Package: slalom Version: 1.6.0 Depends: R (>= 3.4) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rhdf5, scater, testthat License: GPL-2 MD5sum: 76c07e6bd25335b1c7ddd97569ee927b NeedsCompilation: yes Package: SLGI Version: 1.44.0 Depends: R (>= 2.10), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats, BiocGenerics Suggests: GO.db, org.Sc.sgd.db License: Artistic-2.0 MD5sum: dfff03ee3b9f7397bd81b0fa38743465 NeedsCompilation: no Package: slingshot Version: 1.2.0 Depends: R (>= 3.5), princurve (>= 2.0.4), stats Imports: ape, clusterExperiment, graphics, grDevices, igraph, matrixStats, methods, rgl, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, destiny, gam, knitr, mclust, RColorBrewer, rmarkdown, testthat, covr License: Artistic-2.0 MD5sum: f7080eedc58ac571193933bc5808dbcf NeedsCompilation: no Package: slinky Version: 1.2.2 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, curl, dplyr, foreach, httr, stats, utils, methods, readr, rhdf5, jsonlite, tidyr Suggests: GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: a696bfe0964a96ebb9b3fd75d81812de NeedsCompilation: no Package: SLqPCR Version: 1.50.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 9bc228a165da0ae0713484af9968369f NeedsCompilation: no Package: SMAD Version: 1.0.1 Depends: R (>= 3.6.0) Imports: magrittr (>= 1.5), matrixStats, dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 93fb674a64c0702e64b0cd69b128f36b NeedsCompilation: yes Package: SMAP Version: 1.48.0 Depends: R (>= 2.10), methods License: GPL-2 MD5sum: e7f7c7e177651e2116ee07d18352404e NeedsCompilation: yes Package: SMITE Version: 1.12.0 Depends: R (>= 3.3), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr License: GPL (>= 2) MD5sum: 958783774ed22e06691609c65a2bf1fb NeedsCompilation: no Package: SNAGEE Version: 1.24.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: fea3ccc1b2941228ac53614c78d42f5e NeedsCompilation: no Package: snapCGH Version: 1.54.0 Depends: limma, DNAcopy, methods Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL MD5sum: 421d82a4d75f4c064f215b77e2bf7d23 NeedsCompilation: yes Package: snm Version: 1.32.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 582f0ede18333be9c56f09fb59898af6 NeedsCompilation: no Package: SNPchip Version: 2.30.0 Depends: R (>= 2.14.0) Imports: methods, graphics, lattice, grid, foreach, utils, Biobase, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, oligoClasses (>= 1.31.1) Suggests: crlmm (>= 1.17.14), RUnit Enhances: doSNOW, VanillaICE (>= 1.21.24), RColorBrewer License: LGPL (>= 2) MD5sum: 7f754e0adc04950c72bdf08c4944374b NeedsCompilation: no Package: SNPediaR Version: 1.10.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 9b5250e8021dc88cd29b37c1c1a5db03 NeedsCompilation: no Package: SNPhood Version: 1.14.0 Depends: R (>= 3.1), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: 3dcba58f2b36e47a0624d150b80e2bd7 NeedsCompilation: no Package: SNPRelate Version: 1.18.1 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: ef88d834b860e46d7ec53d6c3bdd3383 NeedsCompilation: yes Package: snpStats Version: 1.34.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: b4a3c967936226141b748b94b9d8e008 NeedsCompilation: yes Package: soGGi Version: 1.16.0 Depends: R (>= 3.2.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: 099cf8703b747d9c23f391267c3d035c NeedsCompilation: no Package: SomaticSignatures Version: 2.20.0 Depends: R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE MD5sum: e58cba6da7933d68912454b2b628bcad NeedsCompilation: no Package: SpacePAC Version: 1.22.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 95329db0a49f8763beb15579fd6c86cc NeedsCompilation: no Package: sparseDOSSA Version: 1.8.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE MD5sum: 1ba9d3c5f2a18a6e5885a628f8e805ef NeedsCompilation: no Package: sparsenetgls Version: 1.2.0 Depends: R (>= 3.5.0), Matrix, MASS Imports: methods, glmnet, parcor, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: eb62a6fdb54d805ca4e657806b5e1d2f NeedsCompilation: no Package: SparseSignatures Version: 1.4.0 Depends: R (>= 3.6), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, GenomeInfoDb, ggplot2, gridExtra Suggests: BiocGenerics, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: ef3f68da832a955cea902fe55e383334 NeedsCompilation: no Package: SpatialCPie Version: 1.0.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), dplyr (>= 0.7.6), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), miniUI (>= 0.1.1.1), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), scatterpie (>= 0.1.2), shiny (>= 1.1.0), stats (>= 3.5.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 4f03a2bb6e955655a7d760f494379e9d NeedsCompilation: no Package: specL Version: 1.18.1 Depends: R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.4), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 30acce15f1a222b1a46fb384d064cb63 NeedsCompilation: no Package: SpeCond Version: 1.38.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 249bc80969357bdfbc83be3ab304ce47 NeedsCompilation: no Package: SpectralTAD Version: 1.0.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat License: MIT + file LICENSE MD5sum: 1323e09936b7b05ce36f348196042062 NeedsCompilation: no Package: SPEM Version: 1.24.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: c13851d7ae3e607c65b7c5803953bd4e NeedsCompilation: no Package: SPIA Version: 2.36.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 05858d5358afe0cb844469f5241fb2d8 NeedsCompilation: no Package: SpidermiR Version: 1.14.0 Depends: R (>= 3.0.0) Imports: networkD3, httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 License: GPL (>= 3) MD5sum: 6103a9e30ea7b6bcad2351ebb4ed754f NeedsCompilation: no Package: spikeLI Version: 2.44.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: e798132e48ea94e6d4b72adf02168053 NeedsCompilation: no Package: spkTools Version: 1.40.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: e32f80e2fed6f1f564a83289c806d9dd NeedsCompilation: no Package: splatter Version: 1.8.0 Depends: R (>= 3.4), SingleCellExperiment Imports: akima, BiocGenerics, BiocParallel, checkmate, edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods, scales, scater (>= 1.7.4), stats, SummarizedExperiment, utils, crayon Suggests: BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager, spelling License: GPL-3 + file LICENSE MD5sum: 2b0f09cff1c1378eb497050c8bf87fd6 NeedsCompilation: no Package: splicegear Version: 1.56.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL MD5sum: da2235139f269f64a9d7ffbc7ef13888 NeedsCompilation: no Package: spliceSites Version: 1.31.0 Depends: methods,rbamtools (>= 2.14.3),refGenome (>= 1.6.0),Biobase,Biostrings (>= 2.28.0) Imports: BiocGenerics,doBy,seqLogo,IRanges License: GPL-2 MD5sum: 78ba99a8c7758e468e27e4d8657b5ec8 NeedsCompilation: yes Package: SplicingGraphs Version: 1.24.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.3.21), GenomeInfoDb, GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: e5aa51b3ab50aa58556e05559f6fee1e NeedsCompilation: no Package: splineTimeR Version: 1.12.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 087bdcfe5bd324e43166561b5cccae72 NeedsCompilation: no Package: SPLINTER Version: 1.10.0 Depends: R (>= 3.4.0), grDevices, stats Imports: graphics, ggplot2, seqLogo, Biostrings, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 5c17e4a4d35dbb15fd8210289957752d NeedsCompilation: no Package: splots Version: 1.50.0 Imports: grid, RColorBrewer License: LGPL MD5sum: 2c8f3ef1599114a9a9dfc9827b5d72fe NeedsCompilation: no Package: SPONGE Version: 1.6.2 Depends: R (>= 3.4) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, Suggests: testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel, bigmemory License: GPL (>= 3) MD5sum: c562e4ad67f4b4c95d5b446e1b3b1b8b NeedsCompilation: no Package: spotSegmentation Version: 1.58.0 Depends: R (>= 2.10), mclust License: GPL (>= 2) MD5sum: 893e935858ac11b3273ec21bd6906553 NeedsCompilation: no Package: SQUADD Version: 1.34.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>= 2) MD5sum: e285eaeca7faf352ae6240b30dff480b NeedsCompilation: no Package: sRACIPE Version: 1.0.0 Depends: R (>= 3.6),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 4fff473e90b2561fc312ee61a5ea4423 NeedsCompilation: yes Package: SRAdb Version: 1.46.0 Depends: RSQLite, graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 MD5sum: 227f399b7b8f1c93a2bd8e374da80c89 NeedsCompilation: no Package: sRAP Version: 1.24.0 Depends: WriteXLS Imports: gplots, pls, ROCR, qvalue License: GPL-3 MD5sum: 32f1b0383bfa5e1961a3cd7550c9d7de NeedsCompilation: no Package: SRGnet Version: 1.10.0 Depends: R (>= 3.3.1), EBcoexpress, MASS, igraph, pvclust (>= 2.0-0), gbm (>= 2.1.1), limma, DMwR (>= 0.4.1), matrixStats, Hmisc Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 5f5d012b47227cdcce9fb96c2afe7516 NeedsCompilation: no Package: srnadiff Version: 1.4.0 Depends: R (>= 3.5) Imports: Rcpp (>= 0.12.8), methods, utils, devtools, BiocStyle, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, Rsamtools, GenomicFeatures, GenomicAlignments, ggplot2, BiocParallel LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 1930356d9b2cdcb4f1ec5d7903dac725 NeedsCompilation: yes Package: sscore Version: 1.56.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) MD5sum: 254afef6aa7ebccfbfa5e8eee9bb51ed NeedsCompilation: no Package: sscu Version: 2.14.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 8364ac315f1ff2d0a9ef8ae5d34e6660 NeedsCompilation: no Package: sSeq Version: 1.22.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: a0cf6cbf0c4553d99b106c4024fec9cf NeedsCompilation: no Package: ssize Version: 1.58.0 Depends: gdata, xtable License: LGPL MD5sum: 7d17f1fdee61e0f0c017a2a2d8533404 NeedsCompilation: no Package: SSPA Version: 2.24.0 Depends: R (>= 2.12), methods, qvalue, lattice, limma Imports: graphics, stats Suggests: BiocStyle, genefilter, edgeR, DESeq License: GPL (>= 2) MD5sum: ec400994bc750810cb5652358de4d38d NeedsCompilation: yes Package: ssrch Version: 1.0.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 078f631b72a285cc9900365f94c53e88 NeedsCompilation: no Package: ssviz Version: 1.18.0 Depends: R (>= 2.15.1),methods,Rsamtools,Biostrings,reshape,ggplot2,RColorBrewer,stats Suggests: knitr License: GPL-2 MD5sum: 0291740010847bf4370419650591367d NeedsCompilation: no Package: stageR Version: 1.6.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: 1b9cf571fb3a6b3853fa6ede1dcbe631 NeedsCompilation: no Package: STAN Version: 2.12.0 Depends: methods, poilog, parallel Imports: GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb, Gviz, Rsolnp Suggests: BiocStyle, gplots, knitr License: GPL (>= 2) MD5sum: 09bb714458ce2996b7cebdd743bb78d6 NeedsCompilation: yes Package: staRank Version: 1.26.0 Depends: methods, cellHTS2, R (>= 2.10) License: GPL MD5sum: 9cf9bea816f7bf9b14eb6633e685c42a NeedsCompilation: no Package: StarBioTrek Version: 1.10.0 Depends: R (>= 3.3) Imports: SpidermiR, graphite, AnnotationDbi, e1071, ROCR, MLmetrics, grDevices, igraph, reshape2, ggplot2 Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid License: GPL (>= 3) MD5sum: aad2f6de9be8593284c27883bbb0f54d NeedsCompilation: no Package: Starr Version: 1.40.0 Depends: Ringo, affy, affxparser Imports: pspline, MASS, zlibbioc License: Artistic-2.0 MD5sum: 4ebd6e35c4fbd774b229d172c6aec891 NeedsCompilation: yes Package: STATegRa Version: 1.20.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: 791f82ccec2a724a053db16fdf0de4ee NeedsCompilation: no Package: statTarget Version: 1.14.0 Depends: R (>= 3.3.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown, gWidgets2,gWidgets2RGtk2,RGtk2 License: LGPL (>= 3) MD5sum: a1cd757f8125fb68893927e63977b32f NeedsCompilation: no Package: stepNorm Version: 1.56.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 43370d0d5c7c251b3443035533114e4c NeedsCompilation: no Package: strandCheckR Version: 1.2.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: e91277aa868d4dcadcab553ba630f229 NeedsCompilation: no Package: Streamer Version: 1.30.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: 07e0a31b38c7d1bac26b07d7715800d8 NeedsCompilation: yes Package: STRINGdb Version: 1.24.0 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 852af459f0bf6827166b50f9e4c78387 NeedsCompilation: no Package: STROMA4 Version: 1.8.0 Depends: R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils Suggests: breastCancerMAINZ License: GPL-3 MD5sum: d867e3054739383929d535c47366114b NeedsCompilation: no Package: Structstrings Version: 1.0.3 Depends: R (>= 3.6), S4Vectors, IRanges, Biostrings Imports: methods, assertive, BiocGenerics, XVector, stringr, stringi LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 9fb1eb0dcd8ee8cf8048ae23bdec79f2 NeedsCompilation: yes Package: StructuralVariantAnnotation Version: 1.0.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 3.6.0) Imports: assertthat, Biostrings, stringr, dplyr, methods, rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment License: GPL-3 MD5sum: c6694f42d008a2308d1cc670a12df37d NeedsCompilation: no Package: SubCellBarCode Version: 1.0.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: fbc0ec18e594e7bbaaeded98aa0a8794 NeedsCompilation: no Package: subSeq Version: 1.14.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: 7c8e235019360f80bfb607b98a7d95ca NeedsCompilation: no Package: SummarizedBenchmark Version: 2.2.3 Depends: R (>= 3.5), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble Suggests: iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt License: GPL (>= 3) MD5sum: e68705d2703178560f1a88d808d25e55 NeedsCompilation: no Package: SummarizedExperiment Version: 1.14.1 Depends: R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.17.25), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.13.1) Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat License: Artistic-2.0 MD5sum: 187d8f1c3ef72106c879a918f05adb55 NeedsCompilation: no Package: supraHex Version: 1.22.0 Depends: R (>= 3.3), hexbin Imports: ape, MASS, grDevices, graphics, stats, utils License: GPL-2 MD5sum: 3240782128afb1c78fdc29275638d33c NeedsCompilation: no Package: survcomp Version: 1.34.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, CPE, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: 691520534d33eba80a1a36a6099d3354 NeedsCompilation: yes Package: survtype Version: 1.0.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr License: Artistic-2.0 MD5sum: 71412d425518d026431e1e2815910a68 NeedsCompilation: no Package: Sushi Version: 1.22.0 Depends: R (>= 2.10), zoo,biomaRt Imports: graphics, grDevices License: GPL (>= 2) MD5sum: 5e1d6b719a627e5376aeb07b0e59074d NeedsCompilation: no Package: sva Version: 3.32.1 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 2386dbf4d32da63cdf95d680322b74b8 NeedsCompilation: yes Package: SVAPLSseq Version: 1.10.0 Depends: R (>= 3.4) Imports: methods, stats, SummarizedExperiment, edgeR, ggplot2, limma, lmtest, parallel, pls Suggests: BiocStyle License: GPL-3 MD5sum: 081e1b03e8e5e7cfbab31ed3e4e5e408 NeedsCompilation: no Package: SVM2CRM Version: 1.16.0 Depends: R (>= 3.2.0), LiblineaR, SVM2CRMdata Imports: AnnotationDbi, mclust, GenomicRanges, IRanges, zoo, squash, pls,rtracklayer,ROCR,verification License: GPL-3 MD5sum: d1db763b5ee8b6b2c9ff611723a84725 NeedsCompilation: no Package: SWATH2stats Version: 1.14.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils, biomaRt Suggests: testthat, knitr Enhances: imsbInfer, MSstats, PECA, aLFQ License: GPL-3 MD5sum: 33a9b321934d71a2ea7911d029b02c38 NeedsCompilation: no Package: SwathXtend Version: 2.6.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: 4064834ca97a9aaab22e43c7c107b19a NeedsCompilation: no Package: swfdr Version: 1.10.0 Depends: R (>= 3.4) Imports: stats4, ggplot2, reshape2, stats, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 4e27c02e3839b79035a2c963b69e2cc3 NeedsCompilation: no Package: SwimR Version: 1.22.0 Depends: R (>= 3.0.0), methods, gplots (>= 2.10.1), heatmap.plus (>= 1.3), signal (>= 0.7), R2HTML (>= 2.2.1) Imports: methods License: LGPL-2 MD5sum: f6e8d33f09e824b7dd8cfbac70d70245 NeedsCompilation: no Package: switchBox Version: 1.20.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 MD5sum: 9485b5713f5dd142fb2fa58cb698cdae NeedsCompilation: yes Package: switchde Version: 1.10.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) MD5sum: 352c860f4f9d8494214110aedf58b29e NeedsCompilation: no Package: synapter Version: 2.8.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, knitr, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle License: GPL-2 MD5sum: 2b64d567dd67bdcf3bdf64bac0a0e2ef NeedsCompilation: no Package: synergyfinder Version: 1.10.7 Depends: R (>= 3.6.0) Imports: drc (>= 2.5-12), reshape2 (>= 1.4.1), SpatialExtremes (>= 2.0-2), ggplot2 (>= 2.1.0), grid (>= 3.2.4), lattice (>= 0.20-33), nleqslv(>= 3.0), stats (>= 3.3.0), graphics (>= 3.3.0), grDevices (>= 3.3.0) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: cb889909fbceaf70918c01a409c9b416 NeedsCompilation: no Package: synlet Version: 1.14.0 Depends: R (>= 3.2.0), ggplot2 Imports: doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2 Suggests: knitr, testthat License: GPL-3 MD5sum: 048ac0523519b6ae3d9ab94f22c50371 NeedsCompilation: no Package: SynMut Version: 1.0.1 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: ee9801d0acc3ef8650a7cb8b81b9f09c NeedsCompilation: no Package: systemPipeR Version: 1.18.2 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: BiocGenerics, GenomicRanges, GenomicFeatures (>= 1.31.3), SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, batchtools, yaml Suggests: ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager License: Artistic-2.0 MD5sum: a9e21a5a9f835b67175107fe6036a8b5 NeedsCompilation: no Package: TargetScore Version: 1.22.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 713b143fd0c2cfeecf59d93d412ab509 NeedsCompilation: no Package: TargetSearch Version: 1.40.3 Depends: ncdf4 Imports: graphics, grDevices, methods, stats, tcltk, utils Suggests: TargetSearchData, BiocStyle, knitr License: GPL (>= 2) MD5sum: 5e93b2c66c3b80829c3b3469dce45191 NeedsCompilation: yes Package: TarSeqQC Version: 1.14.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc Suggests: BiocManager, RUnit License: GPL (>= 2) MD5sum: 64224f22c12b68e8a610213a6983f260 NeedsCompilation: no Package: TCC Version: 1.24.0 Depends: R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: fca8112eea20197cfefa1b0c2e35eb7c NeedsCompilation: no Package: TCGAbiolinks Version: 2.12.6 Depends: R (>= 3.5) Imports: downloader (>= 0.4), survminer, grDevices, dplyr, gridExtra, graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0), data.table, EDASeq (>= 2.0.0), edgeR (>= 3.0.0), jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap (>= 1.10.2), R.utils, SummarizedExperiment (>= 1.4.0), genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, GenomeInfoDb, GenomicFeatures, parallel, tools, tidyr, sva, limma, purrr, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, igraph, supraHex License: GPL (>= 3) MD5sum: 7fbe7197b26996103206b09b7c4021f1 NeedsCompilation: no Package: TCGAbiolinksGUI Version: 1.10.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61) Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander License: GPL (>= 3) MD5sum: 5659ea97fe997bdd4013460c59513a39 NeedsCompilation: no Package: TCGAutils Version: 1.4.0 Depends: R (>= 3.6.0) Imports: AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: BiocFileCache, BiocStyle, curatedTCGAData, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, minfi, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox (>= 2.7.5), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, License: Artistic-2.0 MD5sum: 259096a77cd358b89971bd9806f25413 NeedsCompilation: no Package: TCseq Version: 1.8.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: 238ceb170a9261e3a3e8c0dcca57f072 NeedsCompilation: no Package: TDARACNE Version: 1.34.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 45e12f3cf2d2301ac0e5ad0eaacb41db NeedsCompilation: no Package: tenXplore Version: 1.6.0 Depends: R (>= 3.4), shiny, restfulSE (>= 0.99.12) Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils Suggests: org.Hs.eg.db, testthat, knitr License: Artistic-2.0 MD5sum: 7f5c9cc74049ba207a634e77e69a785a NeedsCompilation: no Package: TEQC Version: 4.6.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: fe0e50b70cff7c55f8f0efb0f878d168 NeedsCompilation: no Package: ternarynet Version: 1.28.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) MD5sum: ca477fd797c3c2e465d68beea471b776 NeedsCompilation: yes Package: TFARM Version: 1.6.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, grDevices, stringr, methods, stats Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 6f91d5a29a0274ee1344694c44f9ce21 NeedsCompilation: no Package: TFBSTools Version: 1.22.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0) License: GPL-2 MD5sum: 86c488ad257f26c6dfbe116bb981100f NeedsCompilation: yes Package: TFEA.ChIP Version: 1.4.2 Depends: R (>= 3.3) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 36e6d7a75937c363443e83247c428681 NeedsCompilation: no Package: TFHAZ Version: 1.6.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1d737554beb95e3dcbcf1d78a2ee6f19 NeedsCompilation: no Package: TFutils Version: 1.4.0 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny Suggests: knitr, data.table, GSEABase, testthat, AnnotationDbi, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat License: Artistic-2.0 MD5sum: cdde742d1336acd93fb1a2f0ed74a1d4 NeedsCompilation: no Package: tigre Version: 1.38.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: af4ce4d96d3000ecaa64b6f65c77c023 NeedsCompilation: yes Package: tilingArray Version: 1.62.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 963b2f24edfea1b4c6351745fdb4c697 NeedsCompilation: yes Package: timecourse Version: 1.56.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 3e05749c495fb39c49af5be361e4e16f NeedsCompilation: no Package: timescape Version: 1.8.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 5ef9863c6b75dc7cab6e337e3dd8f611 NeedsCompilation: no Package: TimeSeriesExperiment Version: 1.2.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.19.23), SummarizedExperiment (>= 1.11.6) Imports: dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0), graphics, Hmisc, limma, methods, magrittr, proxy, stats, tibble, tidyr, vegan, viridis, utils Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, License: LGPL (>= 3) MD5sum: ff6f8001e8dbed206a226c83489b948e NeedsCompilation: no Package: TIN Version: 1.16.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 7e16046e63dfdf805d974e4d65aa2c88 NeedsCompilation: no Package: TissueEnrich Version: 1.4.1 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 7396e7da8a154e06c33af846d3bd0815 NeedsCompilation: no Package: TitanCNA Version: 1.22.0 Depends: R (>= 3.5.1) Imports: IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 MD5sum: cd6bd09f869c39c044d50b873d8f5dd9 NeedsCompilation: yes Package: tkWidgets Version: 1.62.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: 63a82dadcb462d25e62fc608eb1f9a44 NeedsCompilation: no Package: TMixClust Version: 1.6.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 7633db1f9553d931f0efd03a8cdeeea9 NeedsCompilation: no Package: TNBC.CMS Version: 1.0.0 Depends: R (>= 3.6.0), e1071, quadprog, SummarizedExperiment Imports: GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma, GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid, stats, methods Suggests: knitr License: GPL-3 MD5sum: 334ca8992244973ec79711cc248de7a6 NeedsCompilation: no Package: TnT Version: 1.6.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: 675d363f8421f4123ed82a93a774a6f7 NeedsCompilation: no Package: tofsims Version: 1.12.0 Depends: R (>= 3.3.0), methods, utils, ProtGenerics Imports: Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth, graphics, grDevices, stats LinkingTo: Rcpp, RcppArmadillo Suggests: EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer Enhances: parallel License: GPL-3 MD5sum: c755f0f4521b6d0d6ea6e8f113be7e14 NeedsCompilation: yes Package: ToPASeq Version: 1.18.1 Depends: R(>= 3.5.0), graphite Imports: Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor LinkingTo: Rcpp Suggests: BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser License: AGPL-3 MD5sum: 581b1a33111e3cab5742a77c975169de NeedsCompilation: yes Package: topconfects Version: 1.0.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr, rmarkdown, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi License: LGPL-2.1 | file LICENSE MD5sum: ea5b0562970d893074b3f14aaf3d6275 NeedsCompilation: no Package: topdownr Version: 1.6.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.2.10), MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.11.4) Suggests: topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 66c9aecc5aeda8dc3ba496326e1bf899 NeedsCompilation: no Package: topGO Version: 2.36.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: 1f8b5fde4b87b14b275958ec40712a79 NeedsCompilation: no Package: TPP Version: 3.12.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, sme, splines, stats, stringr, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 79841b7f3c13fccd119c8d6d53961859 NeedsCompilation: no Package: TPP2D Version: 1.0.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel Suggests: knitr, testthat License: GPL-3 MD5sum: 247c693ff556cb10fdd97ec017becfd0 NeedsCompilation: no Package: tracktables Version: 1.18.0 Depends: R (>= 3.0.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 27834eb1c38a78d2b4a18110bc8c89cc NeedsCompilation: no Package: trackViewer Version: 1.20.5 Depends: R (>= 3.1.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation License: GPL (>= 2) MD5sum: 63e812543098e53249e46415074b25b6 NeedsCompilation: no Package: transcriptogramer Version: 1.6.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: a41827768111c0fd7ef4e0345d7dbd11 NeedsCompilation: no Package: transcriptR Version: 1.12.0 Depends: methods, R (>= 3.3) Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 2e6fb8d3922b8fa74f382f35027e0ad5 NeedsCompilation: no Package: transite Version: 1.2.1 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), ggseqlogo (>= 0.1), gridExtra (>= 2.3), methods, parallel, Rcpp (>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 0.12.18) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0) License: MIT + file LICENSE MD5sum: 66c0e35b4310183492e228a0b5706c0c NeedsCompilation: yes Package: tRanslatome Version: 1.22.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: a134a291903997bd6feeb71756a0164b NeedsCompilation: no Package: TransView Version: 1.28.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: c572af7e22e6181d79bf7d59c3a8fe56 NeedsCompilation: yes Package: traseR Version: 1.14.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 8e936f90626d084548bd4e448de29c8a NeedsCompilation: no Package: treeio Version: 1.8.2 Depends: R (>= 3.4.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.2.3), utils Suggests: Biostrings, ggplot2, ggtree, knitr, phangorn, prettydoc, testthat, tidyr License: Artistic-2.0 MD5sum: 8d37f4b6c76a08699e89e21828ea2b2b NeedsCompilation: no Package: TreeSummarizedExperiment Version: 1.0.3 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors Imports: methods, utils, ape, dplyr, SummarizedExperiment Suggests: ggtree, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: d062e2f9f383b7bc2f17f1e69f5d79be NeedsCompilation: no Package: trena Version: 1.6.1 Depends: R (>= 3.4.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, flare, vbsr, BiocParallel, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown License: GPL-3 MD5sum: 6693f2d6ae895070843c1a4d0547ac35 NeedsCompilation: no Package: Trendy Version: 1.6.4 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 164f8b836abf27eedd41b067240f2e11 NeedsCompilation: no Package: triform Version: 1.26.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: BiocGenerics, IRanges (>= 2.5.27), yaml Suggests: RUnit License: GPL-2 MD5sum: 61db5830197b876cd9d640bcd7a03f40 NeedsCompilation: no Package: trigger Version: 1.30.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: e9d1aef5130094557987635cbe0e2a63 NeedsCompilation: yes Package: trio Version: 3.22.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.5.3) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 05513e6f64ed404eba923616608254ff NeedsCompilation: no Package: triplex Version: 1.24.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs License: BSD_2_clause + file LICENSE MD5sum: 28768817386594eb3fc15f0d055b8fb5 NeedsCompilation: yes Package: tRNA Version: 1.2.2 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, assertive, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 89e8000afeaf7be107abbe282e7ded21 NeedsCompilation: no Package: tRNAdbImport Version: 1.2.2 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, assertive, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: cbc255789f5c36a6569ac0eb91f4d58f NeedsCompilation: no Package: tRNAscanImport Version: 1.4.2 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, assertive, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, GenomeInfoDb, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: GPL-3 + file LICENSE MD5sum: 2c80878b14bdc42ddbdb2e252af1a672 NeedsCompilation: no Package: TRONCO Version: 2.16.2 Depends: R (>= 3.6), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways License: GPL-3 MD5sum: 0a7f378f33f1d7ceec2f80b95b40e10b NeedsCompilation: no Package: TSCAN Version: 1.22.0 Depends: R(>= 2.10.0) Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots Suggests: knitr License: GPL (>= 2) MD5sum: 491016115994ed83297b07684af897e2 NeedsCompilation: no Package: tspair Version: 1.42.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 MD5sum: 0fe6764ba9edb91989fc0d238b12dde5 NeedsCompilation: yes Package: TSRchitect Version: 1.10.12 Depends: R (>= 3.5) Imports: AnnotationHub, BiocGenerics, BiocParallel, dplyr, GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools, IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer, S4Vectors, SummarizedExperiment, tools, utils Suggests: ENCODExplorer, ggplot2, knitr, rmarkdown License: GPL-3 MD5sum: 78603d68a56e73532635518c2f96e714 NeedsCompilation: no Package: TSSi Version: 1.29.0 Depends: R (>= 2.13.2) Imports: methods, BiocGenerics (>= 0.3.2), S4Vectors, Hmisc, minqa, stats, Biobase (>= 0.3.2), plyr, IRanges Suggests: rtracklayer Enhances: parallel License: GPL-3 MD5sum: e73802f58fd8a5199b7f11ec187658f4 NeedsCompilation: yes Package: TTMap Version: 1.6.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 94912c9b54264cb232dba0980ffe4c10 NeedsCompilation: no Package: TurboNorm Version: 1.32.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: d06683056c54c3b734e7877a3e11f49d NeedsCompilation: yes Package: TVTB Version: 1.10.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.7.1), reshape2, Rsamtools, S4Vectors (>= 0.11.11), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 0de5a74af139bcc9791d456a3952c739 NeedsCompilation: no Package: tweeDEseq Version: 1.30.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 328bd849d5545d4448815eda8d57bc55 NeedsCompilation: yes Package: twilight Version: 1.60.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 6d152a6e78dbd5b054dcd1a492d585c9 NeedsCompilation: yes Package: twoddpcr Version: 1.8.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 6d28c4a0a1965a0630e5a4382d97c0c8 NeedsCompilation: no Package: tximeta Version: 1.2.2 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, devtools License: GPL-2 MD5sum: 4e8b25da25dce9808a3a324254b05928 NeedsCompilation: no Package: tximport Version: 1.12.3 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix License: GPL (>= 2) MD5sum: 86fc088b3fd004d82484cd602637ea9e NeedsCompilation: no Package: TxRegInfra Version: 1.4.0 Depends: R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite Imports: methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc License: Artistic-2.0 MD5sum: 0a98c2779acd1d29ecd084e85045555e NeedsCompilation: no Package: TypeInfo Version: 1.50.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 5bf254f161ba0b8610042a08c62c9abf NeedsCompilation: no Package: Ularcirc Version: 1.2.21 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, S4Vectors, shiny, shinyFiles, Sushi, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: d5ae695bc9094651fd26d91a4ebf52f0 NeedsCompilation: no Package: UNDO Version: 1.26.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 67d97af911e0fbcf1966e80baf739023 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.20.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: a875b0d414ebd3efb3a98188424b72ad NeedsCompilation: no Package: UniProt.ws Version: 2.24.2 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 47a5b5909eec76590742779024f46827 NeedsCompilation: no Package: Uniquorn Version: 2.4.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 5aa74d4ee015b2618a9caef436b09852 NeedsCompilation: no Package: universalmotif Version: 1.2.1 Depends: R (>= 3.5.0) Imports: methods, stats, utils, ggplot2, ape, ggtree, ggseqlogo, gtools, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, yaml LinkingTo: Rcpp Suggests: spelling, knitr, BiocStyle, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack Enhances: MotIV, PWMEnrich, rGADEM, motifRG License: GPL-3 MD5sum: fba207c245cdbf2a7f4e5d76521f856c NeedsCompilation: yes Package: uSORT Version: 1.10.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: ef09d8818585ffdd4003c1914c68e7a6 NeedsCompilation: no Package: VanillaICE Version: 1.46.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: Biobase, S4Vectors (>= 0.9.25), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 696d4f2c8aae09dc6a28456bab72f843 NeedsCompilation: yes Package: variancePartition Version: 1.14.1 Depends: R (>= 3.5.0), ggplot2, limma, foreach, scales, Biobase, methods Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL (>= 2) MD5sum: df4aa5df1390dc9b8a854d1aa53dec95 NeedsCompilation: no Package: VariantAnnotation Version: 1.30.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 1.9.9), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges (>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: f0cecd295453bba90ffede4585a6a7a7 NeedsCompilation: yes Package: VariantFiltering Version: 1.20.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 4efa6821bd6877fc2320cbf3a6d22226 NeedsCompilation: yes Package: VariantTools Version: 1.26.0 Depends: S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) License: Artistic-2.0 MD5sum: 85a1a309d99c466cbdc3c60748994bcc NeedsCompilation: no Package: vbmp Version: 1.52.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 21ab3d751b86edfdda86f27a23cd01d6 NeedsCompilation: no Package: VCFArray Version: 1.0.3 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: beb3d98d0012a3f4e62050d24056263c NeedsCompilation: no Package: Vega Version: 1.32.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: d17f38e24edcd024c6650bf651fb2c13 NeedsCompilation: yes Package: VegaMC Version: 3.22.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods, genoset License: GPL-2 MD5sum: 38314360580b97f46f7cb17fc46e15a8 NeedsCompilation: yes Package: VennDetail Version: 1.0.1 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: c794f0585849506aa4b8b2c472875fe0 NeedsCompilation: no Package: vidger Version: 1.4.4 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: 21e26f8243aa88f6f8b1ac13307109bc NeedsCompilation: no Package: viper Version: 1.18.1 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: af2670f7833502314104569352bd73b1 NeedsCompilation: no Package: vsn Version: 3.52.0 Depends: R (>= 3.4.0), Biobase Imports: methods, affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat License: Artistic-2.0 MD5sum: b6164fe0b1b5f91991abd9e948e2bb69 NeedsCompilation: yes Package: vtpnet Version: 0.24.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 51681bfcca401ee6ebb659675afd5773 NeedsCompilation: no Package: vulcan Version: 1.6.0 Depends: R (>= 3.4), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 291cee1c7a3f49263fa5d52a788e5ddf NeedsCompilation: no Package: wateRmelon Version: 1.28.0 Depends: R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest, irlba Enhances: minfi License: GPL-3 MD5sum: 23f2dd01b0492239c6050e8483f3f007 NeedsCompilation: no Package: wavClusteR Version: 2.18.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr, wmtsa Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: b592350ba78ab24461ef82372e07f26d NeedsCompilation: no Package: waveTiling Version: 1.26.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22 License: GPL (>= 2) MD5sum: 414c7fe83b3ad0b3aca89070936e1d4c NeedsCompilation: yes Package: weaver Version: 1.50.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 50bde89ae215d49e504f77727c84af60 NeedsCompilation: no Package: webbioc Version: 1.56.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: c0e717b515a7a27f4371fbabd72f5147 NeedsCompilation: no Package: widgetTools Version: 1.62.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: bd26f959ba3f6851cb0d1ea2346bf0dd NeedsCompilation: no Package: wiggleplotr Version: 1.8.0 Depends: R (>= 3.4) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: e8a1ac4ab6c1eed1878c34273ae48c02 NeedsCompilation: no Package: Wrench Version: 1.2.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 088707f696c3854c4c4631811ab83130 NeedsCompilation: no Package: XBSeq Version: 1.16.0 Depends: DESeq2, R (>= 3.3) Imports: pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, magrittr, roar Suggests: knitr, DESeq, rmarkdown, BiocStyle, testthat License: GPL (>= 3) MD5sum: 48b45d27904653568eb5f44f98fed19a NeedsCompilation: no Package: xcms Version: 3.6.2 Depends: R (>= 2.14.0), methods, Biobase, BiocParallel (>= 1.8.0), MSnbase (>= 2.9.3) Imports: mzR (>= 2.13.3), BiocGenerics, ProtGenerics, lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet (>= 1.5.2), S4Vectors, robustbase Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant, pheatmap Enhances: Rgraphviz, Rmpi, XML License: GPL (>= 2) + file LICENSE MD5sum: a0a40bf4fa93697a67d342c6451cc339 NeedsCompilation: yes Package: XDE Version: 2.30.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: 1edf40b637ab430bbb22f79a1d35d1d8 NeedsCompilation: yes Package: Xeva Version: 1.0.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 709b12e8a7638bd2fc04e4efe5a49da7 NeedsCompilation: no Package: XINA Version: 1.2.0 Depends: R (>= 3.5), Biobase Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 11a837fef20ddc8e6355771f1a8b00af NeedsCompilation: no Package: xmapbridge Version: 1.42.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 2189c4291651059f7c79c3f563427579 NeedsCompilation: no Package: xps Version: 1.44.0 Depends: R (>= 2.6.0), methods, utils Suggests: tools License: GPL (>= 2.0) MD5sum: 878e84b32b583d4957a8585a22adb0eb NeedsCompilation: yes Package: XVector Version: 0.24.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.21.13), IRanges (>= 2.15.12) Imports: methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 044b4a98817641e21cf73a754f3220dc NeedsCompilation: yes Package: yamss Version: 1.10.0 Depends: R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 35ad2405c4a91122902b1e7678c11b99 NeedsCompilation: no Package: YAPSA Version: 1.10.0 Depends: R (>= 3.3.0), GenomicRanges, ggplot2, grid Imports: lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, PMCMR, ComplexHeatmap, KEGGREST, grDevices Suggests: BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d87bbdd5a4d435c4ba8892bfb3d731bf NeedsCompilation: no Package: yaqcaffy Version: 1.44.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 MD5sum: 13ea77a9822e21b130a92bc5ecab266b NeedsCompilation: no Package: yarn Version: 1.10.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: d4cd04eecea5405c57a9c7d79763de11 NeedsCompilation: no Package: zFPKM Version: 1.6.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr License: GPL-3 | file LICENSE MD5sum: 1c309bf1b7bf6f1a32df581d3543b068 NeedsCompilation: no Package: zinbwave Version: 1.6.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: copula, glmnet, BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat License: Artistic-2.0 MD5sum: 7031ddba832cffbed304c94c692c2d9d NeedsCompilation: no Package: zlibbioc Version: 1.30.0 License: Artistic-2.0 + file LICENSE MD5sum: 8e2b5b596ee4d13aca3e195724d28209 NeedsCompilation: yes