a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 3.6), adductData, ExperimentHub, AnnotationHub
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8),
SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6)
R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings,
hypergraph
R (>= 3.6), impute, doParallel, grDevices, dplyr, methods,
ComplexHeatmap
R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData
R (>= 2.5.0), methods, Biobase, BiocManager, GO.db
R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges
BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges
(>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy
R (>= 3.6.0), SummarizedExperiment, ROCR
methods, grDevices, stats, utils, parallel, edgeR, limma,
AnnotationDbi
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
0.22.1), BSgenome, IRanges
R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.4), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
R (>= 2.3.0), methods, GenomicRanges, abind, parallel
R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase
R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr
R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 4.0.0), methods, utils, graphics, stats
R (>= 4.0), reticulate, methods, SummarizedExperiment
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 3.5.0), IRanges, GenomicRanges, Gviz
R (>= 3.5.0), igraph, poweRlaw, latex2exp, RSpectra, Rdpack
R (>= 4.0), shiny, igraph, shinyBS, pathview, DT
R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24),
GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula
ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel,
Biobase, metafor, methods
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 4.1.0), biomaRt, SummarizedExperiment
R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5),
SummarizedExperiment (>= 1.19.5)
R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23),
GenomeInfoDb, GenomicRanges, foreach, iterators, methods,
parallel, locfit
R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio
R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>=
1.38.2), SummarizedExperiment (>= 1.8.1)
methods, MultiAssayExperiment, R (>= 4.1.0)
R (>= 2.14.0), Biobase, binom, methods, stats
ProtGenerics, BiocGenerics, BiocParallel, EBImage, graphics,
methods, S4Vectors (>= 0.27.3), stats
R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 4.0), SingleCellExperiment, Matrix
R (>= 3.6), SingleCellExperiment, magrittr, methods, stats,
tibble, utils
R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment
R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML,
ggplot2, rmarkdown
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest,
DT, RPMM
R (>= 4.2), ggplot2, SingleCellExperiment
Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors,
ensembldb, AnnotationFilter, data.table
R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll,
parallel
R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19),
BiocParallel
R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData
R (>= 4.1.0), generics, methods, S4Vectors,
MultiAssayExperiment, BiocParallel, survival
R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>=
1.15.4), BiocGenerics
R (>= 3.6), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
R (>= 3.5.0), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.10), methods, tools, stats, genefilter
brglm, doParallel, foreach, GenomicRanges, methods,
splitstackshape
R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags,
ggplot2, gridExtra
R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
2.17.8), limma
R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy
R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych
R (>= 4.1.0), SummarizedExperiment, RaggedExperiment,
BiocSingular, HDF5Array
R (>= 3.5.0), methods, topGO, GenomicRanges
R (>= 3.5.0), methods, grid, graphics, stats, grDevices
R (>= 4.1), methods, AnnotationFilter, S4Vectors
R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges,
BiocParallel
R (>= 3.5.0), minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylationEPICmanifest
R (>= 2.14), igraph, shiny, arules, methods
R (>= 4.1), BiocGenerics, SummarizedExperiment
R (>= 4.0.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 3.3.0), shiny, shinyjs, CRISPRseek
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 3.5.0), GenomicRanges, SummarizedExperiment
SummarizedExperiment, GenomicRanges, IRanges, S4Vectors,
rtracklayer
R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1)
R (>= 4.0), EBImage, SingleCellExperiment, methods
R (>= 3.5.0), SummarizedExperiment, ggplot2
R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats,
parallel
R (>= 3.5.0), AnnotationDbi, BiocParallel,
SummarizedExperiment, limma
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
R (>= 2.13.0), methods, graphics, parallel, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.27.6),
R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.43.4), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),
IRanges (>= 2.17.3)
MatrixGenerics (>= 1.5.3), DelayedArray (>= 0.17.6)
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment,
knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend,
psych, sva
S4Vectors (>= 0.23.18), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R(>= 4.0.0), R.utils, DESeq2, BiocParallel
BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11),
AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18)
R (>= 4.0), GenomicRanges, SummarizedExperiment
R (>= 3.5), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges
R (>= 4.1.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10)
R (>= 4.0.0), methods, stats, utils, graphics, Rcpp
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 3.5.0), parallel, doParallel, foreach,
SummarizedExperiment, stats
R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0),
GenomicRanges
R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>=
1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>=
1.5.2)
R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2,
foreach, Rtsne, igraph
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2)
R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment,
cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14),
flexmix (>= 2.3.15)
R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment
Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6),
BiocFileCache (>= 1.5.1)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.21.3)
R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment,
SpatialExperiment, TreeSummarizedExperiment
R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2, RCurl, jsonlite, BiocStyle
BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.4.0),
SummarizedExperiment, tibble
methods, LiquidAssociation, parallel, doParallel, stats,
Hmisc, utils
R (>= 4.2.0), S4Vectors, IRanges, GenomicRanges, grid
R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram
R (>= 4.1), mclust, BiocParallel, SummarizedExperiment
R (>= 2.15.0), methods, Biobase, rrcov, flowCore
R (>= 2.11.0), flowCore, flowViz,flowClust
R (>= 3.2), methods, flowCore, flowViz, flowStats
R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>=
0.5.32)
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
R (>= 4.1), survcomp, biomaRt, iC10, AIMS
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2),
MatrixGenerics, GenomicRanges (>= 1.31.16),
SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>=
1.17.29), rtracklayer (>= 1.25.3)
R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges,
biomaRt, ggplot2
R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
R (>= 4.1), Matrix, MultiAssayExperiment, glmnet
circlize, GenomicRanges, graphics, R (>= 4.0)
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome,
data.table
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)
R (>= 3.2), penalized, Iso, survival, methods,
graph,stats,glmnet,mvtnorm
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 3.5.0), Biobase, SummarizedExperiment
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 3.5.0), GenomicRanges, BiocGenerics
GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges,
magrittr, ggplot2, methods, stats,utils ,knitr,dplyr
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, BiocIO
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16)
R (>= 3.6), utils, curl, rhdf5, R6, grid
InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
4.1.0)
R (>= 3.6), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
R (>= 3.5.0), Biostrings, GenomicAlignments, BiocParallel,
hiAnnotator
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer, graphics, GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>=
2.17.1)
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R (>= 3.6), methods, Biobase, BiocParallel
R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
MultiAssayExperiment, SummarizedExperiment,stats
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 3.5.0), methods, BiocGenerics, grid
R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment,
edgeR, S4Vectors
R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest
R (>= 4.1), mclust, BiocParallel, survival
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats,
utils
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2),
S4Vectors (>= 0.33.3)
R(>= 4.1.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.4), regioneR, GenomicRanges, methods
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 4.0), ggplot2, parallel, stats, S4Vectors
R (>= 3.5.0), S4Vectors, SingleCellExperiment,
SummarizedExperiment, methods, rhdf5, BiocIO
R (>= 4.1), ExperimentHub, AnnotationHub
S4Vectors, adabag, GenomicRanges, R (>= 4.1)
R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
R (>= 2.10), convert, graph, limma, marray, methods
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>=
1.6.0)
R (>= 3.5), BiocParallel, Matrix, methods, stats
RUnit, BiocGenerics, BiocParallel, GenomicRanges,
SummarizedExperiment
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
R (>= 2.15), grDevices, graphics, methods, stats, utils
R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 4.0), methods, CAMERA, xcms (>= 1.35)
R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea,
ggplot2, ggrepel
R (>= 4.0.0), DESeq2, limma, locfit, splines
R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table,
Biobase, digest
R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings
R (>= 4.1.0), methylclockData, devtools, quadprog
R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods
R (>= 3.5.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R (>= 4.0), SummarizedExperiment, SingleCellExperiment,
TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment
R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment,
mia (>= 0.99), ggplot2, ggraph (>= 2.0)
R (>= 4.1), MultiAssayExperiment (>= 1.8.3)
R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2
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
methods, BiocGenerics (>= 0.15.3), GenomicRanges,
SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>=
1.1.9)
R (>= 3.2), Biobase (>= 2.22.0), miRcompData
R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
R (>= 4.0), SummarizedExperiment, topGO, stats
data.table, parallel, utils, stats, R (>= 4.1)
R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 4.2.0), SummarizedExperiment (>= 1.3.81)
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors,
SummarizedExperiment
R (>= 3.6), SummarizedExperiment, S4Vectors
R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
R (>= 4.2.0), igraph, reticulate, pandaR, yarn
R(>= 3.5.0), keras, limma, e1071, SingleCellExperiment
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2,
limma, rhdf5, foreach, Rfast, octad.db, stats, httr,
ExperimentHub, AnnotationHub, Biobase, S4Vectors
R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
dplyr, optimalFlowData, rlang (>= 0.4.0)
R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10),
AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4)
R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
R (>= 3.6), BiocParallel, GenomicFeatures,
SummarizedExperiment, data.table, methods
R (>= 4.1.0), SummarizedExperiment, S4Vectors
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.5.0), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.3.0), methods, ggplot2, gridExtra
R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome,
BiocParallel
R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2, Hmisc
R (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1),
BiocGenerics, S4Vectors
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges
(>= 1.28.4)
R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph,
graph, graphite
R (>= 4.1), Biobase, SingleCellExperiment, MAST
biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb,
yeastExpData
R (>= 2.14.0), GenomicAlignments, affy, RPA
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 3.6), BiocGenerics, SummarizedExperiment
R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1)
R (>= 3.5.0), methods, BiocGenerics, Biostrings
reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
testthat
R (>= 3.5), Biostrings, BiocGenerics,methods
R (>= 4.1), parallel, GenomicRanges, Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11),
Biostrings (>= 2.47.6), Biobase
R (>= 4.1), GenomicRanges, parallel, doParallel, foreach,
doRNG, methods
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq
R (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2,
ComplexHeatmap
R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2,
multtest, Biostrings, BSgenome, ChIPpeakAnno
R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet,
SummarizedExperiment
R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0)
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.6.0), GenomicRanges, IRanges, methods
R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments
R (>= 3.0.2), methods, GenomicRanges, abind
methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9),
GenomicRanges, Modstrings
R(>= 3.5.0), ggplot2, pathview, edgeR, methods
R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData
R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2),
gplots, grid, gridExtra, limma, matrixStats, methods,
illuminaio, methylumi, plyr
boot, SummarizedExperiment, fission, knitr, methods
methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz
R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods,
rmarkdown
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),
Biostrings (>= 2.47.6), R (>= 3.5.0)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2)
R (>= 3.4.0), biclust, SummarizedExperiment
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.37.0)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel,
reshape2, phangorn, sangerseqR, gridExtra, shiny,
shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle,
logger
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 3.6), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4),
tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
parallel, preprocessCore, splines, splines2, xgboost,
SCATEData, Rtsne, mclust
R (>= 4.0), S4Vectors, SingleCellExperiment,
R (>= 3.6), SummarizedExperiment, dynamicTreeCut,
SingleCellExperiment
SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1),
shiny
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19
R (>= 4.0), methods, epivizr, SummarizedExperiment
R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
2.15.0), methods
R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>=
1.20.3)
R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10),
Rsamtools (>= 1.31.2), SummarizedExperiment, methods
methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>=
1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R
(>= 3.0.0)
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R(>= 3.6.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
R (>= 4.0), SummarizedExperiment, SingleCellExperiment,
DelayedArray, Biobase
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate
R (>= 3.5.0), BiocGenerics, SummarizedExperiment
R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>=
1.29.1)
GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
Rgraphviz (>= 2.3.7)
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 4.0), ggplot2, ggridges, SummarizedExperiment,
BiocGenerics
R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape,
ggplot2, RColorBrewer, stats
R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 4.1.0)
R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors,
BiocGenerics, methods, UpSetR, rlang, stringr, utils,
BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo,
crayon, tibble
R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),
GenomicRanges (>= 1.41.5), Biobase
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
GenomicRanges, rtracklayer, VariantAnnotation,
StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>=
4.0)
GenomicRanges, rtracklayer, BiocGenerics,
StructuralVariantAnnotation, R (>= 4.0)
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2),
ggplot2, plyr, openxlsx
R (>= 3.0), methods, DESeq2, edgeR, baySeq, ROC
R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data
R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 4.2.0), AnVIL, MultiAssayExperiment
R (>= 4.0.0), ttservice, SingleCellExperiment
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6.0), e1071, quadprog, SummarizedExperiment
R (>= 3.6), EpiDISH, limma, nnls, quadprog
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.5.0), grDevices, methods, GenomicRanges, grid, Rcpp
R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq2,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
R (>= 3.5.0), GenomicRanges, IRanges,
BSgenome.Hsapiens.UCSC.hg19
R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18),
Biostrings
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 2.15.2), methods, BiocGenerics, Biobase
methods, utils, RSQLite, BiocGenerics (>= 0.13.8)
R (>= 4.2.0), methods, BiocGenerics, S4Vectors
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
R (>= 4.0.0), ggplot2, limma, BiocParallel
R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>=
1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>=
1.99.0)
R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>=
1.13.0), GenomicRanges,
R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1),
VariantAnnotation (>= 1.13.29)
R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)
R (>= 4.0), GenomicRanges, IRanges, ggplot2
R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel,
foreach
R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene,
zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.6.0), GenomicRanges, ggplot2, grid
R (>= 3.4), methods, SummarizedExperiment,
SingleCellExperiment
methods, graphics, grid, Biobase, annaffy, mpm, genefilter,
limma, multtest, glmnet, gplots
methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils,
graphics, stats
Biobase, graphics, grDevices, methods, multtest, stats, tcltk,
utils
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
Biobase, QDNAseq, ggplot2, grid, stats, utils, methods,
grDevices, GenomicRanges
Biobase, grDevices, graphics, methods, stats, splines, utils
bit, DNAcopy, tilingArray, waveslim, cluster, aCGH, snapCGH
checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS,
Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment,
stats, SummarizedExperiment, utils
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest
(>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils, zlibbioc
affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi,
BiocManager, R2HTML, xtable
stats, methods, S4Vectors, SummarizedExperiment,
SingleCellExperiment, Matrix, tibble, rlang
SingleCellExperiment, SummarizedExperiment, S4Vectors, scater,
stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue,
dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2,
ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid,
grDevices, graphics, utils, pbapply
Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest
rmarkdown (>= 2.5), tools, methods, ggplot2, GGally, dplyr,
rjson, shiny, shinydashboard, DT, stats, utils, tximport (>=
1.17.4), cowplot, rlang, Rcpp
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
Biostrings, IRanges, GenomicRanges, GenomicAlignments,
Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm,
splines, graph, RBGL, stringr, stats, methods, graphics,
GenomeInfoDb, S4Vectors
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, knitr, ggplot2,
gridExtra, utils
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
mia, stats, CVXR, DescTools, Hmisc, MASS, Rdpack, S4Vectors,
SingleCellExperiment, SummarizedExperiment,
TreeSummarizedExperiment, doParallel, doRNG, dplyr, emmeans,
energy, foreach, lme4, lmerTest, magrittr, nloptr, parallel,
rlang, rngtools, tibble, tidyr, utils
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb,
IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings,
GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster,
mclust
igraph, Biobase, survival, MASS, stats, RColorBrewer
assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2,
rentrez, reshape2, covr, ape, vegan, dplyr, magrittr,
MultiAssayExperiment, SummarizedExperiment, S4Vectors (>=
0.23.19), XML, forcats, scales, lattice, glmnet, tsne, plotROC,
DT, utils, limma, methods, stats, tibble, biomformat, umap,
Matrix, GUniFrac
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), httr
DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors,
interactiveDisplayBase, httr, yaml, dplyr
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocManager, biocViews, BiocCheck, graph,
AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>=
1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger
(>= 1.3.0), XML, RCurl
AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures,
GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges,
methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>=
0.23.10), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
stats, utils, methods, futile.logger, jsonlite, httr,
rapiclient (>= 0.1.3), tibble, tidyselect, tidyr, rlang, shiny,
DT, miniUI, htmltools, BiocManager
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVIL, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools,
utils, stats
GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2,
ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2,
methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis,
Rsamtools, HybridMTest
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat,
SingleCellExperiment, magrittr, SummarizedExperiment, topGO,
methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang
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.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
Biobase, BiocGenerics, Biostrings, GenomicRanges, Hmisc,
IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools,
ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods,
rJava, stats, svMisc, utils, sendmailR, bitops
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
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
AnnotationDbi, bit64, circlize, cluster, corrplot, data.table,
dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics,
grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db,
pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats,
stringr, tidyr, UpSetR, utils, VennDiagram, yaml
BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods,
mvtnorm, PepsNMR, plyr, quadprog, ropls, stats,
SummarizedExperiment, utils, Matrix, zoo
BiocParallel, GenomicAlignments, GenomicFeatures,
GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma,
S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr,
fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer,
scales, grid, ggplot2, mGSZ, utils
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle,
igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid,
graphics, pbmcapply
Biostrings, GenomicRanges, IRanges, graphics, grDevices,
methods, stats, utils
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp
(>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize,
grid, grDevices, graphics
gtools, GenomicRanges, projectR, TFBSTools, GeneOverlap,
msigdbr, tidyverse, gplots, motifmatchr, chromVAR,
GenomicFeatures, IRanges, fgsea, rGREAT, JASPAR2016,
Homo.sapiens, Mus.musculus, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, stringr, dplyr
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats,
motifStack, preseqR, utils, KernSmooth, edgeR
BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges,
GenomicAlignments, GenomeInfoDb, SummarizedExperiment,
Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2,
ggrepel, dplyr, limma, methods
methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors,
IRanges, GenomicRanges, GenomicAlignments, Rsamtools,
GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub,
scales, matrixStats
BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table,
ggplot2, grDevices, graphics, grid, motifStack, rappdirs,
stats, testthat, utils, lifecycle
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
DelayedArray, DelayedMatrixStats, data.table, graphics,
grDevices, GSEABase, Matrix, methods, mixtools, R.utils, shiny,
stats, SummarizedExperiment, BiocGenerics, utils
abind, assertive, BiocFileCache, BiocGenerics, colorspace,
data.table, edgeR, ggplot2, ggrepel, graphics, grDevices, grid,
gridExtra, limma, magrittr, matrixStats, methods,
MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang,
R.utils, readxl, S4Vectors, scales, stats, stringi,
SummarizedExperiment, tidyr, tools, utils
GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
reshape2, scales, coda, foreach, ggplot2, methods, utils,
graphics, stats
VariantAnnotation, Rsamtools, biomaRt, GenomicRanges,
S4Vectors, utils, stats, grDevices, graphics
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
BiocGenerics, BiocParallel, data.table, dplyr, tidyr,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr,
knitr, methods, BiocParallel, robustbase, BiocStyle,
ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils,
grDevices, rlang
cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges,
graphics, grDevices, magrittr, plyr, proxy, RColorBrewer,
rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors,
tibble, tidyr, vegan, viridis, utils
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2,
graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3),
S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment,
viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat,
reshape2, BiocParallel, hexbin
methods, glmGamPoi, scran, scuttle, stats, utils,
SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstantools (>= 2.1.1)
utils, methods, parallel, reticulate, dir.expiry,
basilisk.utils
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, BiocParallel, scuttle,
ResidualMatrix, ScaledMatrix, beachmat
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, heatmaply, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
Rcpp (>= 1.0.4.6), stats, purrr, scater, scran,
SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix,
assertthat, mclust, RCurl, DirichletReg, xgboost, utils,
ggplot2, scales, BiocFileCache, BiocSingular
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
parallel, MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices,
GenomicRanges, IRanges, Biostrings
Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats
methods, DelayedArray (>= 0.15.14), BiocGenerics, Matrix, Rcpp
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
ggplot2, SingleCellExperiment, data.table, stats, utils,
graphics, compiler
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
cli, edgeR, BiocParallel, methods, progressr, stats,
SummarizedExperiment, utils
stats, stats4, utils, methods, phyloseq,
TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR,
DESeq2, limma, ALDEx2, SummarizedExperiment, MAST, Seurat,
ANCOMBC, NOISeq, dearseq, metagenomeSeq, corncob, MGLM,
ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges,
graphics, cowplot, tidytext
GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt,
jsonlite, methods, dplyr, data.table, sjmisc, grDevices,
graphics, stats, utils, rslurm, rhdf5
R.utils, data.table, curl, RCurl, digest, methods, stats,
utils, dplyr, RSQLite, graph, Biobase
stats, utils, GEOquery, graphics, BiocGenerics, illuminaio
tidyr, tibble, dplyr, plyr, matrixStats, stats, ggplot2,
methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, Gviz
R.oo, httr, DT (>= 0.3), dplyr (>= 0.7.2), shiny (>= 1.0.5),
AnnotationDbi, methods, Biobase, geNetClassifier, org.Hs.eg.db,
DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<=
1.01), visNetwork, htmlwidgets, plyr, tibble
biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr,
tools, codetools, methods, utils, knitr
httr, whisker, readr, dplyr, utils, methods, memoise
DT, shiny, jsonlite, graph, tidyr, visNetwork, igraph, utils,
methods, BiocBaseUtils
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs,
filelock, curl, httr
Rgraphviz, geneplotter, graph, BiocGenerics, methods
Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr,
rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges,
ggplot2, SummarizedExperiment, DBI, GenomicFeatures,
curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
stats, utils, futile.logger, parallel, snow, codetools
BiocFileCache, BiocManager, biocViews, tibble, magrittr,
methods, rlang, stringr, rvest, dplyr, xml2, readr, httr,
htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL, graph,
rorcid
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat
bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1)
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, jsonlite,
lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
stats, stringr, tools, withr, yaml
utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr,
httr, digest, BiocFileCache, rappdirs, xml2
stats, utils, grDevices, lattice, BiocParallel, glmnet, rms,
precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot,
imager, topGO, xlsx
stringr, synaptome.db, clusterCons, fgsea, grid, methods,
scales, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db, rSpectral,
WGCNA, ggplot2, ggrepel
WGCNA, dynamicTreeCut, matrixStats, sva, RColorBrewer,
ComplexHeatmap, ggplot2, ggrepel, patchwork, reshape2, igraph,
ggnetwork, intergraph, networkD3, ggnewscale, NetRep, stats,
grDevices, graphics, utils, methods, BiocParallel, minet,
GENIE3, SummarizedExperiment
igraph (>= 1.0.1), AnnotationDbi, Biobase
BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr,
utils, stats, RColorBrewer, Hmisc, psych, knitr, rmarkdown,
markdown
Biobase, methods, e1071, grDevices, graphics,
MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats,
SummarizedExperiment, utils
methods, utils, grDevices, graphics, stats, crayon
igraph, cluster, psych, stringr, GenomicRanges, MASS, scran
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, limma
grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.23.19), 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
readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools,
data.table, Biobase, GenomicRanges, IRanges, BiocGenerics,
VariantAnnotation, DelayedMatrixStats, SummarizedExperiment,
GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats,
rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools,
BiocParallel
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer,
parallel, betareg, lokern, Formula, globaltest
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8),
BiocGenerics, grDevices, stats, graphics
SummarizedExperiment, ExperimentHub, methods, grid, graphics,
stats, grDevices, circlize, testthat, ComplexHeatmap(>=
1.99.8), ggplot2, matrixStats, gtools, reshape2,
preprocessCore, randomcoloR, V8, limma
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb,
S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage,
utils
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr,
GenomicRanges, ggforce, stringr, plyranges, methods, utils,
magrittr
doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist,
bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot,
dplyr, rlang, GenomicRanges
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
Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder
(>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>=
1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils,
grDevices, GenomicState (>= 0.99.7)
data.table, lsa, methods, S4Vectors, utils, BiocFileCache,
shiny
plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt,
Biostrings, parallel, utils, stats,
BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges,
GenomeInfoDb, IRanges, S4Vectors, data.table
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
GenomicRanges, parallel, IRanges, stats, Rsamtools,
GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods
methods, utils, stats, matrixStats, BiocGenerics, S4Vectors,
IRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges,
Biostrings, Rsamtools, rtracklayer
IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>=
0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2),
permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel,
BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5
BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2,
WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra,
biovizBase, e1071, methods, grDevices, stats, utils
devtools, stringi, gtools, stats, utils, SummarizedExperiment,
Biostrings, IRanges
matrixStats, limma, doRNG, BiocGenerics, utils,
GenomicFeatures, AnnotationDbi, stats
utils, methods, Matrix, S4Vectors, IRanges
gplots, methods, grDevices, stats, SummarizedExperiment
AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics,
Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb,
GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr,
Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr,
tibble, tidyr, utils, zeallot
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges,
reshape2, methods, BioNERO
BiocGenerics, BiocParallel, BSgenome, data.table,
DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb,
GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>=
2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr,
Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), som,
stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart,
survival, Biobase, phenoTest, circlize, plyr, graphics, stats,
utils, grDevices, R.oo, R.methodsS3, httr
cluster, impute, limma, ConsensusClusterPlus, grDevices,
survival
combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree,
Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors,
utils, VariantAnnotation, vcfR
Biobase, irlba, Matrix, matter, magrittr, mclust, nlme,
parallel, signal, sp, stats4, utils, viridisLite
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools,
rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
ggridges, graphics, grDevices, grid, gridExtra, magrittr,
Matrix, matrixStats, methods, nnls, purrr, RColorBrewer,
reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales,
scater, stats
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
BiocFileCache, RColorBrewer, cBioPortalData, genefilter,
gplots, grDevices, stats, utils, openxlsx
BiocParallel, BiocSet, dplyr, lmom, fitdistrplus, magrittr,
methods, mixtools, Rcpp (>= 1.0.7), stats,
SummarizedExperiment, tibble, TreeSummarizedExperiment, tidyr,
glue, generics, rlang, goftest
BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb,
GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment,
RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment,
stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils
utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite,
rapportools, basilisk, reticulate, shinyBS, shinycssloaders,
rintrojs, markdown
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack
(>= 0.7)
Rcpp, matrixStats, stats, SIMLR, BiocParallel
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
grDevices, graphics, matrixStats, doParallel, digest, methods,
reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot,
enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne,
withr, scater (>= 1.14.4), scran, dbscan, DelayedArray,
stringr, ComplexHeatmap, multipanelfigure, circlize
dplyr, tibble, stringr, Biostrings, Rcpp, reshape2, methods,
rlang (>= 0.3), purrr, Matrix, S4Vectors, BiocGenerics, tidyr,
forcats, progress, stats, utils, generics, glue
methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr,
ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings
(>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr,
zlibbioc
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue,
memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect,
lubridate
Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater,
stringr, irlba, data.table, glue, pbapply, umap, Rtsne,
reticulate, fastmatch, matrixStats, ggplot2, BiocParallel,
SummarizedExperiment, fgsea
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
tiff, graphics, stats, utils, reshape2, parallel, doParallel,
grDevices, matrixStats, FME, SpatialTools, sp, vioplot,
FactoMineR, Hmisc
BiocNeighbors, ggplot2, scater, viridis, cowplot,
SummarizedExperiment, SingleCellExperiment, tidyr, magrittr,
dplyr, ggridges, stats, purrr, methods, BiocParallel,
BiocGenerics
BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
topicmodels, slam, maptpx, igraph, xtable, gplots
httr, curl, jsonlite, utils, tools, shiny, DT, rjsoncons
methods, scales, 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, fastcluster
BiocParallel, broom.mixed, dirmult, dplyr, edgeR,
fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp,
purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment,
survival, tibble, tidyr, utils
DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors,
methods, SingleCellExperiment, SummarizedExperiment, ggplot2,
rlang, grDevices, patchwork, reshape2, BiocParallel, stats,
dplyr
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr,
GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr,
ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3,
stats, SummarizedExperiment, S4Vectors, utils, methods
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb,
GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3),
stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1),
Rsamtools (>= 2.4.0), rlang (>= 0.4.0)
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
limma, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,kpmt,ggplot2,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
BiocGenerics, zlibbioc, Rcpp (>= 0.11.0)
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
ChIC.data (>= 1.11.1), caTools, methods, GenomicRanges,
IRanges, parallel, progress, randomForest, caret, grDevices,
stats, utils, graphics, S4Vectors, BiocGenerics,
genomeIntervals, Rsamtools
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments,
RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db,
org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr,
BiocStyle, checkmate, gtools, magick
AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb,
GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra,
MASS, 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 (>= 0.23.10), stats, stringr, utils
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
AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>=
2.47.6), DBI, dplyr, ensembldb, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, RBGL, Rsamtools,
SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices,
graph, graphics, grid, InteractionSet, KEGGREST, matrixStats,
multtest, regioneR, rtracklayer, stats, utils
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, 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
AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges,
GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots,
graphics, grDevices, gtools, methods, plotrix, dplyr, parallel,
magrittr, RColorBrewer, rtracklayer, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene, utils
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
graphics, stats, utils, methods, survival
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
shiny, colourpicker, shinyjs, rtracklayer, shinyFiles,
shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders,
Matrix, plotly, shinydashboard, colorRamps, kableExtra,
viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2,
ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs,
qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr,
tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble,
methods, jsonlite, edgeR, stats, graphics, grDevices, utils,
S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr,
forcats, Rcpp, coop, matrixTests, DelayedArray
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb,
IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals,
mvtnorm
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
XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx,
igraph, circlize, graph, stats, utils, grDevices, graphics,
methods, biomaRt, rJava
dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork,
ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat,
tidygraph, expm, Matrix
bitops,gplots,grDevices,som,
dplyr,gridExtra,png,stringr,S4Vectors, IRanges,
GenomeInfoDb,graphics, stats, utils
dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2,
edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2,
ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb,
universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
Biostrings, gwascat, BSgenome,
stats, tools, utils, methods, S4Vectors, rlang, magrittr,
dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges,
ShortRead, Rsamtools, Rbowtie2, Rhisat2
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, propr, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph,
scales, scran (>= 1.14.6), graphics, methods, stats, utils,
reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices,
rhdf5, rlang
grid, genefilter, utils, dplyr, tidyr, rlang, ranger
BSgenome, GenomicRanges, seqinr, e1071, Biostrings,
GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome,
Biostrings, utils
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix,
matrixStats, methods
mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally,
ggplot2, plotly, methods, utils, stats, sna, grDevices,
graphics, Biobase, gplots, MSnbase
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, howmany, locfdr, matrixStats, graphics, parallel,
BiocSingular, kernlab, stringr, S4Vectors, grDevices,
DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp,
edgeR, scales, zinbwave, phylobase, pracma, mbkmeans
AnnotationDbi, downloader, DOSE (>= 3.23.2), dplyr, enrichplot
(>= 1.9.3), GO.db, GOSemSim, gson (>= 0.0.7), magrittr,
methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang,
scales, stringr, tibble, tidyr, stats, methods,
SingleCellExperiment, SummarizedExperiment, matrixStats,
S4Vectors, proxy, httr, utils
methods, rhdf5, data.table, flowCore, SummarizedExperiment,
matrixStats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors, exomeCopy
IRanges, GenomicRanges, SummarizedExperiment, pracma,
regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics,
utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings,
methods
dplyr, stats, utils, grDevices, plotly, karyoploteR,
CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics
GenomicRanges, IRanges, S4Vectors, BiocParallel, methods,
magrittr, stats, pheatmap, gridExtra, grDevices
BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq,
IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr,
GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics,
methods, shiny, shinyFiles, shinyjs, grid, openxlsx
BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges,
S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR,
gdsfmt, grDevices, lattice, limma, methods, plyr, qqman,
rappdirs, reshape2, stats, utils
BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
grDevices, simpleCache, fitdistrplus
affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma,
graphics, stats, utils, STRINGdb, SummarizedExperiment, minet,
rmarkdown
BiocParallel, cluster, methods, gplots, graphics, grDevices,
RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tools, utils, rhdf5
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, stringr, tibble, tidyr, dplyr, devtools
utils, graphics, stats, methods, reshape2, ggplot2, ggtree,
patchwork, igraph, Biostrings
BiocManager, rmarkdown, GenomeInfoDb, S4Vectors,
AnnotationDbi, graphics, stats, utils, methods, magrittr,
ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.5.4), 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, foreach, doParallel,
irlba
methods, ggplot2, reshape2, dplyr, gridExtra, plotly,
circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel,
GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils,
Matrix, grid, stats, SummarizedExperiment, plyr, Gviz
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix, BB,
reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics,
methods, SummarizedExperiment
hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors,
GenomicRanges, stats, corrplot
AnnotationHub, BiocParallel, bumphunter, ExperimentHub,
GenomicRanges, IRanges, lmerTest, methods, stats, utils
GenomicRanges, parallel, grid, ggplot2, reshape2, scales,
DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach,
coda
tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16),
gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2,
stringr, modeest, edgeR, limma, vioplot, methods, stats, utils,
ape, phylolm, matrixStats, grDevices, graphics
AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel,
grDevices, gplots, IRanges, GenomicFeatures, XVector,
methylPipe, GO.db, S4Vectors, GenomeInfoDb
circlize (>= 0.4.14), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,
matrixStats, foreach, doParallel, codetools
BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr,
RSQLite, Biobase, ProtGenerics, xml2, IRanges, Spectra (>=
1.5.17), MsCoreUtils, MetaboCoreUtils
data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr,
rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio,
scales, shinydashboard, shinyjs, stats, tibble, grid
org.Hs.eg.db, org.Mm.eg.db, dbscan, fpc, factoextra, Biobase,
BiocFileCache, parallel, doParallel, foreach,
SummarizedExperiment, biomaRt, AnnotationDbi, methods, dplyr,
scran, scater, pheatmap, ggplot2, gridExtra,
SingleCellExperiment, stats, utils, scales, grDevices,
graphics, Rtsne, GEOquery, clusterProfiler, stringr, tools,
rlang
slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment,
SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume
(>= 0.9.1), methods, pbapply, matrixStats, BiocParallel,
TrajectoryUtils, igraph, distinct
matrixStats, gplots, grDevices, methods, graphics, stats,
utils
Biobase, ALL, graphics, stats, utils, cluster
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
Biobase, GSVA, gdata, genefu, limma, matrixStats,
randomForest, stats, utils, methods
GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats,
SummarizedExperiment, BiocParallel, graph, methods, pheatmap,
survival, topGO, graphics, grDevices
data.table, grDevices, clue, cluster, gplots, BiocGenerics (>=
0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP,
GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy,
colorspace, reshape2, ggplot2, methods, exomeCopy,
GenomicAlignments, diagram
methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
GenomeInfoDb
regioneR, IRanges, Rsamtools, SummarizedExperiment,
VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges,
cn.mops, rhdf5, utils
matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges,
Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges,
CopyhelpeR, GenomeInfoDb, futile.logger
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics,
piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods,
stats, utils, graphics, grDevices, lsa, data.table, crayon,
glue, rlang, bench
ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix,
methods, MultiAssayExperiment, pals, reshape2,
SingleCellExperiment, SummarizedExperiment, transport
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2,
scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics,
stats, methods, compositions, mvtnorm
CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
rlang, stringr, utils, visNetwork
dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, stats,
parallel, tibble, tidyr, irlba, ComplexHeatmap, circlize, grid,
scales, utils, rlang, Rfast
rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils,
methods, ragg
S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
parallel, genefilter, grDevices, stats, graphics
methods, corpcor, BiocParallel, ggplot2, plyr
BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges,
S4Vectors, stringr
BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15),
GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats,
stringr, utils
BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb,
Rbwa, readr, stats, stringr, utils
AnnotationDbi, BiocGenerics, Biostrings, BSgenome,
crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb,
GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix,
MatrixGenerics, methods, rtracklayer, S4Vectors, stats, utils,
VariantAnnotation
basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics,
Biostrings, IRanges, methods, randomForest, reticulate,
stringr, utils, XVector
parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray,
GenomeInfoDb, GenomicRanges, dplyr, keras, mltools
DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures,
BiocManager, BSgenome, AnnotationDbi, hash
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
BiocManager, cli, crisprBase, crisprBowtie, crisprScore,
crisprDesign, crisprViz, rlang, tools, utils
BiocGenerics, Biostrings, BSgenome, GenomeInfoDb,
GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges,
methods, S4Vectors
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils,
lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats,
VGAM, parallel, graphics, limma, beanplot
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods,
S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod,
utils
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2,
grDevices, stats, utils
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
AnnotationDbi, AnnotationHub, binr, cowplot, data.table,
dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics,
highcharter, htmltools, httr, limma, methods, parallel,
pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang,
scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble,
tools, utils
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
stats, pscl, qvalue, BiocParallel, methods, knitr,
SpatialExperiment, SummarizedExperiment
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats,
rappdirs, BiocFileCache
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
Biobase, flowCore, flowDensity, flowClust, cytometree,
ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats,
utils
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment,
flowCore, Biobase, Rcpp, BiocNeighbors
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods,
rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix,
SummarizedExperiment, tibble, tidyr
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, speedglm, stringr, strucchange, tibble,
ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices
Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap,
circlize, ashr, data.table, BiocParallel, dplyr, stats,
magrittr, rlang, S4Vectors
SpatialExperiment, S4Vectors, BiocParallel, HDF5Array,
DelayedArray, RColorBrewer, viridis, utils,
SummarizedExperiment, tools, graphics, raster, grDevices,
stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny,
shinydashboard, matrixStats, rhdf5, nnls
gplots, tools, flowCore, grDevices, stats, utils, matrixStats,
methods
cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>=
4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL,
Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite,
dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats,
tibble
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils,
biomaRt, motifStack, httr
stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr,
SummarizedExperiment, GenomicAlignments, stringr, plyr,
VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics,
methods, limma, bumphunter, Biostrings, reshape2, cowplot,
utils
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,
plyr
Biobase, MSnbase, DAPARdata (>= 1.28.0), utils, highcharter,
foreach
basilisk, BiocFileCache, BiocParallel, data.table, dplyr,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, ggpubr,
ggrepel, grid, IRanges, magrittr, megadepth, methods,
plyranges, readr, reticulate, rtracklayer, S4Vectors, stringr,
SummarizedExperiment, tidyr
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
stats, methods, assertthat, graph, pcalg, purrr, tidyverse,
Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR,
epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2,
graphite, reshape2, dplyr, magrittr, glue, Rgraphviz,
harmonicmeanp, org.Hs.eg.db, logger, shadowtext
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
matrixStats, methods, patchwork, parallel, pbapply, reshape2,
rlang, scattermore, stats, statmod, survey, tibble, viridisLite
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2,
pcaPP, apcluster, graphics
shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT,
ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE,
igraph, grDevices, graphics, stats, utils, GenomicRanges,
IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2,
org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler,
methods, sva, RCurl, enrichplot, colourpicker, plotly,
heatmaply, Harman, pathview, apeglm, ashr
methods, DBI, S4Vectors, IRanges, XVector
stats, methods, ggplot2, foreign, graphics, BiocStyle,
Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4,
sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2,
gridExtra
Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment,
ComplexHeatmap, grid, parallel, BiocParallel, grDevices,
graphics, stats, methods, utils
methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats,
GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr,
utils, graphics, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
SummarizedExperiment, ggseqlogo, gridExtra, data.table,
GenomeInfoDb, readxl
broom, dplyr, magrittr, Matrix, purrr, rlang, stats, stringr,
tibble, tidyr, tidyselect, withr
GenomicRanges, data.table, stringr, diffr, dplyr, methods,
rjson, utils, R.utils, foreach, withr, rtracklayer,
GenomeInfoDb, settings, filehash
tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers,
webchem, purrr, ttgsea, PRROC, reticulate, stats
checkmate, data.table, DESeq2, edgeR (>= 3.13.4),
GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment
Rcpp (>= 1.0.2),GenomicFeatures, parallel, foreach, S4Vectors,
doParallel, Rsamtools (>= 1.31.2), GenomicAlignments,
heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges,
plyr, plotly, utils,viridis
graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
utils, methods, Biobase, BiocGenerics, broom, circlize,
ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2,
dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices,
knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang,
scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr,
tibble
graphics, grDevices, methods, stats, utils
methods, matrixStats (>= 0.60.0), sparseMatrixStats, Matrix
(>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10)
methods, utils, DelayedArray, HDF5Array, BiocSingular,
rTensor, DelayedRandomArray, irlba, Matrix, einsum,
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2,
tictoc
matrixStats, stats, truncdist, base64enc, ggplot2
stats, MASS, Matrix, ggplot2, gridExtra, methods
Rcpp, basilisk, assertthat, reticulate, irlba
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
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 (>=
0.23.19), stats, utils
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
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, reshape2, S4Vectors (>=
0.9.38), scales, utils
BiocParallel, BiocGenerics, ChIPpeakAnno, data.table,
DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges,
plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19),
SummarizedExperiment, tools, utils
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats,
methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0)
methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp
(>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba,
pcaMethods, Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix,
jsonlite, tools, DESeq2, methods
BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb,
GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats,
utils
Biobase, GEOquery, impute, limma, pheatmap, plyr, scales,
snpStats, sva, swamp, stats, methods, utils, bnstruct,
RColorBrewer, grDevices
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
zoo (>= 1.8-3), data.table, magrittr, dplyr, tidyr, rlang, mzR
(>= 2.18), signal, bit64, reticulate, ggplot2, RSQLite, DBI,
ape, phangorn, pracma, RMSNumpress, Rcpp
RColorBrewer, amap, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, lattice,
systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel,
parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods,
graphics, ggrepel, apeglm, ashr, GreyListChIP
stats, DiffCorr, psych, igraph, BiocGenerics
flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma,
edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats,
methods, utils, grDevices, graphics, ComplexHeatmap, circlize,
grid
methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel,
foreach, stats, BANDITS, Matrix, SingleCellExperiment,
SummarizedExperiment, ggplot2
graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils
Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma,
csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb,
BiocGenerics, grDevices, graphics, stats, utils, Rcpp,
rtracklayer
grDevices, stats, methods, Matrix, MASS, checkmate, expm,
igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq,
GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap,
ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr,
matrixStats, IRanges, ensembldb, viridisLite
BiocParallel, BiocSingular, SummarizedExperiment,
SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats,
parallel, scran, grDevices, stats, methods
Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr,
methods, utils
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, zip, reshape2
Rcpp, Rfast, stats, SummarizedExperiment,
SingleCellExperiment, methods, Matrix, foreach, parallel,
doParallel, doRNG, ggplot2, limma, scater
methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2,
pheatmap, grDevices, ggrepel, ggridges, stats, utils,
SummarizedExperiment, SingleCellExperiment, S4Vectors
utils, stats, speedglm, MASS, data.table, splines, arm,
rtracklayer, benchmarkme, tibble, matrixStats, fastDummies,
graphics
utils, stats, grDevices, rtracklayer, multcomp, calibrate,
graphics
parallel, Rcpp, RcppRoll, betareg, grDevices, graphics,
methods, stats, utils
ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, minfi,
missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils,
S4Vectors, methods, graphics, SummarizedExperiment
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb,
methods, mvtnorm, stats, parallel
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
dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats,
utils, methods
bamsignals, GenomicRanges, IRanges, Rsamtools,
GenomicAlignments, BiocBaseUtils, S4Vectors
biomaRt, data.table, utils, stats, Biostrings,
SummarizedExperiment, VariantAnnotation, AnnotationDbi,
GenomeInfoDb, IRanges, GenomicRanges, methods
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
prodlim, matrixStats
AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim
(>= 2.23.1), methods, qvalue, reshape2, stats, utils
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
MASS, IRanges, BSgenome, grDevices, parallel
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors,
IRanges, GenomicRanges, SummarizedExperiment, BiocParallel,
DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR,
R.utils, dqrng, beachmat, scuttle
utils, RSQLite, UniProt.ws, biomaRt,ensembldb,
BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr,
tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode
progeny, easierData, dorothea (>= 1.6.0), quantiseqr, ROCR,
grDevices, stats, graphics, ggplot2, ggpubr, DESeq2, utils,
dplyr, matrixStats, rlang, BiocParallel, reshape2, rstatix,
ggrepel, coin
clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang,
stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi
Biobase (>= 2.50.0), BiocFileCache (>= 1.14.0), BiocGenerics
(>= 0.36.0), BiocParallel (>= 1.24.1), biomaRt (>= 2.46.0),
Biostrings (>= 2.58.0), edgeR (>= 3.32.0), GenomeInfoDb (>=
1.26.0), genomeIntervals (>= 1.46.0), GenomicAlignments (>=
1.26.0), GenomicRanges (>= 1.42.0), SummarizedExperiment (>=
1.20.0), graphics, IRanges (>= 2.24.0), LSD (>= 4.1-0), locfit,
methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 2.6.0),
S4Vectors (>= 0.28.0), ShortRead (>= 1.48.0), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
methods, graphics, BiocGenerics, IRanges (>= 1.13.9),
aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings,
AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager
methods, splines, sva, snm, qvalue(>= 1.99.0), MASS
methods, graphics, stats, utils, locfit, Rcpp
R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR,
DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db,
org.Mm.eg.db, limma, DOSE, AnnotationDbi
gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo,
igraph, plyr, MASS, RCurl, methods
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),
htmlwidgets, plotly, DT
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
graphics, stats, GenomicRanges, S4Vectors, IRanges, limma,
edgeR, methods, SummarizedExperiment, BiocGenerics, utils
GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
methods, parallel, stats, utils, IRanges, GenomeInfoDb,
S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), 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, reshape2, ggpubr, rtracklayer,
DelayedArray
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
BiocGenerics, Biostrings, BSgenome, BiocParallel,
BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges,
jsonlite, motifmatchr, Matrix, rtracklayer, Rcpp, S4Vectors,
stats, utils
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db,
KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR,
graphite, hwriter, limma, methods, pathview, safe
aplot (>= 0.1.4), DOSE (>= 3.16.0), ggnewscale, ggplot2,
ggraph, graphics, grid, igraph, methods, plyr, purrr,
RColorBrewer, reshape2, rlang, stats, utils, scatterpie,
shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.4)
BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils,
methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr,
heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices,
magrittr
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>=
0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics,
Biostrings (>= 2.47.9), curl
S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment,
GenomeInfoDb, stats
stats, methods, utils, GenomicRanges, BiocGenerics,
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi,
data.table, Rcpp
AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation,
GenomicRanges, IRanges, GenomeInfoDb, ggplot2, htmltools,
methods, plotly, reshape2, rmarkdown, rtracklayer, stats,
stringr, utils, BiocGenerics
EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges,
rstatix, ggpubr, methods, stats, utils, dplyr
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr, Matrix
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
Rcpp, magrittr, data.table, SummarizedExperiment, methods,
GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools,
bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5,
Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap,
grDevices
data.table, doParallel, EntropyExplorer, graphics, stats,
grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA
AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table,
doParallel, doSNOW, downloader, dplyr, ELMER.data,
ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures,
GenomicRanges, GEOquery, ggplot2, graphics, grDevices, impute,
IRanges, limma, methods, parallel, plyr, progress, R.matlab,
RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats,
SummarizedExperiment, tibble, tidyr, utils
minfi, bumphunter, isotree, robustbase, ggplot2,
GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment,
stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt,
BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi,
AnnotationHub, ExperimentHub, reshape2, grid, ensembldb,
gridExtra, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel
BoolNet, e1071, gtools, stats, igraph, utils, lattice,
latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph,
mnem, latex2exp
GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors,
IRanges, viridisLite, graphics, plotrix, grDevices, stats,
methods
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, Rcpp (>=
0.11.0), ggplot2, grid, graphics, utils
methods, utils, httr, xml2, curl, GenomicFeatures,
GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache,
S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport
epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4),
GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb
epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson,
methods, BiocGenerics
S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0),
OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb
git2r, epivizrServer, GenomeInfoDb, BiocGenerics,
GenomicFeatures, S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr
rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb,
Biobase, shiny, BiocParallel, IRanges, AnnotationDbi
Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
rJava, magrittr, digest, BSgenome, AnnotationDbi,
GenomicAlignments, GenomicFeatures, R.utils, GenomeInfoDb,
BiocGenerics, S4Vectors, IRanges, rmarkdown, tools,
VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics,
stats, utils, parallel, corrplot, BiocManager, motifmatchr
grDevices, dplyr, ggplot2, GSEABase, GSVA,
SingleCellExperiment, ggridges, msigdbr, stats, BiocParallel,
Matrix, UCell, broom, reshape2, patchwork, MatrixGenerics,
utils, rlang, stringr, data.table, SummarizedExperiment,
methods
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class,
prabclus, mclust, kableExtra
GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls,
limma, matrixStats, RBGL, prodlim, graph, methods, utils,
stats, doParallel, foreach, affxparser, GenomicRanges,
S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings,
glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport,
fgsea
stats, utils, methods, ewceData, dplyr, ggplot2, reshape2,
limma, stringr, HGNChelper, Matrix, parallel,
SingleCellExperiment, SummarizedExperiment, DelayedArray,
BiocParallel, orthogene (>= 0.99.8), data.table
stats, methods, grDevices, graphics, utils
utils, S4Vectors, BiocManager, curl, rappdirs
methods, ExperimentHub, BiocManager, DBI, httr, curl
shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs
BiocIO, broom, ComplexUpset, csaw, dplyr, edgeR,
EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions,
ggforce, ggrepel, ggside, glue, grDevices, grid, Gviz,
InteractionSet, IRanges, limma, methods, patchwork,
RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales,
stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram
methods, graphics, grDevices, stats, utils
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2,
rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex,
tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT,
clusterProfiler, org.Hs.eg.db
affy, MASS, Biobase (>= 1.13.41), methods, graphics
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
ape, data.table, dynamicTreeCut, methods, R.utils, rJava,
stats, stringr, utils
methods, graphics, grDevices, stats, BiocGenerics, S4Vectors,
IRanges
ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment,
stats, mclust
fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap,
grDevices, stats, utils
FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph,
grid, intergraph, stringr, clusterProfiler, data.table,
grDevices, methods, network, scales, sna, utils, stats,
SingleCellExperiment, pathwayPCA, Matrix
stats, plyr, VariantAnnotation, SummarizedExperiment,
rtracklayer, GenomicRanges, methods, IRanges, foreach,
doParallel, parallel
tcltk, graphics, grDevices, stats, utils
SingleCellExperiment, methods, stats, utils, irlba, TSCAN,
SC3, matrixStats
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache,
curl
igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2,
RColorBrewer, png, methods, stats, utils, graphics, grDevices
Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
cowplot, grid, fastmatch, Matrix, utils
foreach, doParallel, GenomicRanges, IRanges, Rsamtools,
parallel, S4Vectors
withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors,
GenomicFeatures, dplyr, rlang, patchwork, ggplot2,
BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble,
tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges,
progress, purrr, glmnet, methods
graphics, stats, utils, methods, abind, gtools, qvalue,
S4Vectors, IRanges, SummarizedExperiment, GenomicRanges,
matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
basilisk, bambu, Biostrings, BiocGenerics, circlize,
ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges,
GenomicFeatures, GenomeInfoDb, ggplot2, ggbio, grid, gridExtra,
igraph, jsonlite, magrittr, Matrix, parallel, reticulate,
Rsamtools, rtracklayer, RColorBrewer, SingleCellExperiment,
SummarizedExperiment, scater, S4Vectors, scuttle, stats, scran,
stringr, MultiAssayExperiment, tidyr, utils, withr, zlibbioc,
ggplot2, flowCore, plyr, changepoint, knitr, reshape2,
RColorBrewer, scales, methods, graphics, stats, utils,
rmarkdown
colorRamps, abind, BiocParallel, graphics, stats, utils,
plotly, shiny
methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid
BiocGenerics, methods, Biobase, graph, flowCore, parallel
Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>=
2.3.4), S4Vectors
flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics,
stats,methods
flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos,
gplots, RFOC, flowWorkspace (>= 3.33.1), methods, stats,
grDevices
Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices,
methods, stats, stats4
effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2,
igraph, Matrix, matrixStats, stats, utils, visNetwork,
htmlwidgets, grDevices, methods, stringr, stringi, Rdpack,
data.table (>= 1.9.5), gridExtra,
Biobase, graphics, grDevices, methods, rrcov, stats, feature,
flowCore
rrcov,flowCore, graphics, methods, stats, utils
flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny,
methods, graphics, stats, utils
stats, utils, colorRamps, ConsensusClusterPlus, dplyr,
flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices,
magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML
BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace,
ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods,
grDevices, graphics, stats, cluster, utils, KernSmooth,
lattice, ks, RColorBrewer, rrcov, corpcor, mnormt
utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
flowCore, methods, flowViz, stats, flowClust
stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
Biobase, BiocGenerics, cytolib (>= 2.3.9), XML, ggplot2,
graph, graphics, grDevices, methods, stats, stats4, utils,
RBGL, tools, Rgraphviz, data.table, dplyr, scales, matrixStats,
RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4),
DelayedArray, S4Vectors
RUnit, methods, ChemmineR, BiocGenerics, parallel
clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr,
ontologyIndex, purrr, RecordLinkage, stringr, textclean,
tictoc, tidygraph, tidyr, vroom
AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt,
BSgenome, cowplot, DelayedArray (>= 0.5.11),
DelayedMatrixStats, extraDistr, generics, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges,
grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods,
OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer,
rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools,
utils, VGAM
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
shiny, fda, doParallel, GenomicAlignments, Rcpp, methods,
foreach, parallel, GenomeInfoDb, Rsamtools, grDevices,
graphics, stats, RColorBrewer
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster,
fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest,
methods, SummarizedExperiment, stats, S4Vectors
BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges,
httr, IRanges, jsonlite, methods, VariantAnnotation
AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
stats, utils, methods, ggplot2, tidyr, expm, Rcpp,
RcppParallel, gdsfmt
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
Biobase, limma, RobustRankAggreg, ggplot2,
SummarizedExperiment, grid, rmarkdown, grDevices, graphics,
methods, ComplexHeatmap, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR,
stringr, graphics, stats, affxparser, data.table
shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,
clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,
survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,
BiocParallel
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
magrittr, glue, memoise, jsonlite, data.table, rlang,
lubridate, utils, stringr, SummarizedExperiment, Biobase,
tibble, tidyr, S4Vectors, httr, rappdirs, bit64
graphics, grDevices, methods, stats, tcltk, utils, xtable
BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>=
1.31.10), GenomicFeatures (>= 1.31.5), Biostrings,
VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28),
GenomeInfoDb, Biobase
biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools,
ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats,
tibble, utils
utils, GenomicRanges, org.Hs.eg.db, BiocGenerics,
GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer
utils, methods, stats, Biobase, BiocGenerics
BiocGenerics, AnnotationDbi, annotate, Biobase, graphics,
methods, stats, survival, grDevices
amap, impute, mclust, limma, graphics, stats, utils
snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR,
IRanges, GenomicRanges, data.table,grDevices, graphics,stats,
utils, methods
plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods,
grDevices, stats, graphics
igraph, snow, ape, grDevices, graphics, stats, utils,
data.table
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt,
GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools,
SNPRelate, data.table, graphics, grDevices, igraph, Matrix,
methods, reshape2, stats, utils
AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize,
colorspace, colourpicker, ComplexHeatmap, ComplexUpset,
dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce,
ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph,
matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang,
rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders,
shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools,
utils, viridis, visNetwork
data.table, dplyr, graphics, networkD3, RColorBrewer,
SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle,
org.Rn.eg.db
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), Rcpp (>= 0.12.14)
Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb,
GenomicRanges, IRanges, dplyr, data.table, parallel,
doParallel, foreach, methods, S4Vectors, stats, numbers, utils
stats, stats4, utils, RCurl, GenomeInfoDbData
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
stats, httr, xml2, jsonlite, utils, rlang, readr,
GenomicRanges, IRanges, dplyr, rappdirs, tibble
data.table, ggplot2, reshape2, methods, utils, Biostrings,
plyr, dplyr, scales, broom, GenomeInfoDb, stats
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO,
rtracklayer (>= 1.51.5), biomaRt (>= 2.17.1), Biobase (>=
2.15.1)
GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25),
VariantAnnotation (>= 1.27.9), GenomeInfoDb
AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures,
GenomeInfoDb, methods, IRanges, RBGL, S4Vectors
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
grDevices, stats, utils, plyr, gridExtra, lsr, parallel,
ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache,
IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub,
rhdf5, DelayedArray, HDF5Array
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable, irlba
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders,
reticulate, stats
AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings,
DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>=
2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>=
2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis,
data.table, BSgenome, GenomeInfoDb, VariantAnnotation
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
DT, htmltools, factoextra, heatmaply, maptools, pheatmap,
scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap,
GEOquery, impute, grDevices, stats, graphics, utils
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, lmerTest, dplyr, stringr, grDevices,
graphics, GGally, rlang, ggplot2, SeuratObject
readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr,
limma, curl, R.utils
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel,
parallel, foreach, reshape2, dplyr
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
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
plyr, scales, hexbin, data.table, RColorBrewer, gridExtra,
rlang
gdsfmt, ggrepel, grDevices, RColorBrewer, rlang, scales,
SeqArray (>= 1.32.0), stats
Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices,
seqmagick, grid, methods, statebins, ggtree (>= 1.17.1)
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
ggside, grid, methods, stats
ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods,
purrr, rlang, ggfun (>= 0.0.6), yulab.utils, tidyr, tidytree
(>= 0.3.9), treeio (>= 1.8.0), utils, scales, stats, cli
ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>=
0.3.9), cli
methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices,
stats, utils, IRanges (>= 2.13.12)
Biobase, changepoint, data.table, genefilter, graphics,
GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats
DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats,
methods, graphics, grDevices, xtable, tools, brew, stringr,
RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment,
stats, jsonlite, methods, S4Vectors
Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics,
DelayedArray, HDF5Array, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, methods, stats, utils,
splines, rlang
SummarizedExperiment, biomaRt, futile.logger, futile.options,
forcats, utils, dplyr, glue, readr, digest, httr, ggplot2,
survminer, reshape2, stringr, parallel, methods
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
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
AnnotationDbi, ape, bnlearn, Category, DT, doParallel,
foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db,
org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics,
reshape2, stats, utils
grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics,
Biostrings, GenomeInfoDb, methods, GenomicAlignments,
GenomicFeatures, IRanges, rtracklayer, pracma, colorspace,
S4Vectors
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
mgcv, graphics, stats, utils, AnnotationDbi,
GO.db,BiocGenerics
org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL,
graph, Matrix, corpcor, Rcpp
GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler,
parallel
AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils
methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>=
1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz
plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable
BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools,
ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils,
stats, GenomeInfoDb
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
Deriv, DescTools, digest, pryr, stringr, BiocGenerics
futile.logger, checkmate, patchwork, reshape2, data.table,
matrixStats, Matrix, GenomicRanges, RColorBrewer,
ComplexHeatmap, DESeq2, circlize, progress, utils, methods,
stringr, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings,
GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats,
gridExtra, limma, tidyselect, readr, grid, tidyr, dplyr, stats,
grDevices, graphics, magrittr, tibble, viridis, colorspace,
biomaRt, topGO
cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify,
grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap,
purrr, rlang, stats, tibble, tidyr, utils
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, purrr
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics,
KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods,
S4Vectors, stats, utils
dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud,
stringr, gridExtra, rlang, grDevices, graphics, stats, methods
cluster, doParallel, foreach, matchingR, nsga2R, survival,
proxy, stats, methods,
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, stats, utils, graphics, S4Vectors, IRanges, Biobase,
SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel,
BiocParallel, SingleCellExperiment, sparseMatrixStats,
DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular
circlize (>= 0.4.8), GetoptLong, grDevices, utils
Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats,
BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6),
stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb,
Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr,
tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang
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), ensembldb
(>= 2.11.3), 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), graphics, grDevices, stats, utils
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges
(>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi,
BiocFileCache, snpStats, VariantAnnotation, AnnotationHub
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth, data.table
GWASTools, survival, VariantAnnotation, parallel, matrixStats,
SummarizedExperiment, stats, utils, SNPRelate
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache,
tools, utils, digest, shiny, miniUI, DT
utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>=
0.31.5), S4Vectors, IRanges
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
assertthat, biomaRt, Biobase, BiocGenerics, checkmate (>=
2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats,
forcats, GenomicRanges, ggplot2, ggrepel (>= 0.9), IRanges,
lifecycle, limma, magrittr, matrixStats, methods,
MultiAssayExperiment, purrr, R6, Rdpack, rlang, stats,
S4Vectors, tidyr, utils
Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape,
dendextend, ggplot2, mclust, patchwork, dplyr, grDevices,
methods, stats
foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2,
scales, methods
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, GenomeInfoDb, GenomicRanges, stats, IRanges,
grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel,
R.utils, readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq,
KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats,
S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, rhdf5,
grid, ggpubr, gridExtra, ggExtra, data.table, multiHiCcompare,
GenomeInfoDb
HiContactsData, InteractionSet, GenomicInteractions,
GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, BiocGenerics,
methods, rhdf5, Matrix, vroom, tibble, tidyr, dplyr, glue,
stringr, reticulate, ggplot2, ggrastr, scales
methods, utils, HilbertVis, png, grDevices, circlize (>=
0.3.3), IRanges, GenomicRanges, polylabelr
R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges,
S4Vectors, XVector, Biostrings, GenomicFeatures,
BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices,
stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
coin, stats, limma, grDevices, utils, graphics,
preprocessCore, servr, DelayedArray, matrixStats, methods,
S4Vectors
ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap,
dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment,
ggrepel
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, GenomeInfoDb
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
utils, stats, scales, stringr, tibble, shiny, data.table
dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble,
utils, stringr, magrittr, caret, corrplot, ggplot2, pROC,
PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
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
edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices,
graphics, methods
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
shiny, ssrch, S4Vectors, SummarizedExperiment, utils
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr,
scales, rlang, httr, openxlsx, htmltools, reshape2, reactable,
msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny
methods, grid, graph, hypergraph, Rgraphviz, stats4
irlba, stats, cluster, graphics, SummarizedExperiment,
BiocParallel
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
stats, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d, utils
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2,
ggplot2 (>= 2.0.0), scales, ROCR, dplyr, DT, limma, methods,
UpSetR, markdown
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap,
pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma,
GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0),
shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel,
knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc,
methods
dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>=
1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1),
grDevices, grid, idr (>= 1.2), IRanges (>= 2.18.0), magrittr
(>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0),
stats, stringr (>= 1.3.1), utils
methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment
methods, BiocGenerics, httpuv, utils, rtracklayer,
VariantAnnotation, RColorBrewer, httr
methods, slam, lpsymphony, fdrtool, BiocGenerics
Matrix, parallel, foreach, aricode, LiblineaR, SparseM,
ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster,
parallelDist, cluster, dendextend, DescTools, plyr, scales,
pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment,
SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils
tools, Biobase, hwriter, methods, vsn, stats, utils, e1071
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats,
ggfortify, grDevices, methods, Matrix, utils, graphics,
gridExtra, grid, lattice, Rsamtools, survival, BiocParallel,
GenomicAlignments, parallel
S4Vectors, stats, utils, SummarizedExperiment, methods,
pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind,
BiocParallel, viridis, dplyr, magrittr, DT, igraph,
SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph,
tidygraph, ggplot2, data.table, sf, concaveman, tidyselect,
distances, MatrixGenerics
STRINGdb, Biostrings, igraph, graphics, utils, seqinr
utils, R6, data.table, curl, httr, Rlabkey (>= 2.3.1),
Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots,
plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown,
preprocessCore, flowCore, flowWorkspace, digest
methods, stats, graphics, grid, lattice, grDevices
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, phyclust, Matrix, fastcluster,
parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin,
caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus,
future, foreach, doParallel, Seurat, BiocGenerics,
SummarizedExperiment, SingleCellExperiment, tidyr, parallel,
coda, gridExtra, argparse
stats, grDevices, utils, graphics, pbapply, matlab, png,
raster, grid, uwot, gtools, Biobase, generics, parallel,
methods, xgboost
AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq,
depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges,
GenomicFeatures, ggplot2, IRanges, limma,
magrittr,methods,parallelly, plyranges, preprocessCore,
readr,reshape2, RSQLite, stats,S4Vectors, utils
pROC, deSolve, rootSolve, KernSmooth, gdata, GenomicFeatures,
GenomicRanges, IRanges, BiocGenerics, GenomicAlignments,
Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer,
SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, GenomeInfoDb
grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>=
0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils,
svglite, htmltools, clisymbols, jsonlite, RColorBrewer,
fontawesome
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
config, golem, shiny, DT, shinydashboard, shinyFiles,
shinycssloaders, data.table, fs, dplyr, tidyr, circlize,
colourpicker, dendextend, factoextra, ggplot2, plotly, plyr,
shinyFeedback, shinyalert, tibble, umap, visNetwork,
wordcloud2, readxl, htmlwidgets, colorspace, signal, scales,
htmltools, ComplexHeatmap, grDevices, stats, tools, utils,
biomaRt, rlang, fmsb, igraph
seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), IRanges,
seqinr, graphics, grDevices, stats, utils, grid, methods, DBI,
RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq,
DESeq2
Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr,
S4Vectors, IRanges, GenomicRanges, SummarizedExperiment,
methods
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer,
stats
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
Rcpp (>= 1.0.0), MCL, anocva, Polychrome, RColorBrewer,
colorspace, AnnotationDbi, ggplot2, org.Hs.eg.db, org.Mm.eg.db,
pheatmap, AdaptGauss, DEsingle,DrImpute, Matrix, Seurat,
SingleCellExperiment, clusterProfiler, ggpubr, ggraph, igraph,
mixtools, scater, scran, stats, methods, grDevices, graphics,
utils, knitr
utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
DT
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
ggrepel, colourpicker, igraph, vipor, mgcv, graphics,
grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize,
grid
AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs,
S4Vectors, shiny, shinydashboard, shinyjs, utils
methods, S4Vectors, IRanges, shiny, SummarizedExperiment,
SingleCellExperiment, ggplot2, DT, stats, colourpicker,
shinyAce
dplyr, magrittr, methods, quadprog, readr, readxl, stringr,
tibble, tools, utils, pracma, WriteXLS
IsoCorrectoR, readxl, tcltk2, tcltk, utils
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), tximeta (>=
1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr,
tibble, XVector, BiocGenerics, RCurl, Biobase
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
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify,
grDevices, methods, Matrix, BiocParallel,utils, stats
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics,
memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase,
digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi,
grDevices, VariantAnnotation
methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector
(>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics,
grDevices, utils, apcluster
methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
AnnotationDbi,graph,DBI, graph, grDevices, methods, stats,
tools, utils
data.table, BiocParallel, sqldf, stats, grid, grDevices
aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics,
grDevices, matrixStats, stats, utils, foreach, doParallel,
parallel, shiny, shinycssloaders, ade4, factoextra, DT
stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab,
rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML,
praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3),
limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>=
4.4.0), gridExtra
curl, igraph, foreach, doParallel, sortable, dplyr, data.tree,
graphics, grDevices, parallel, RColorBrewer, Rfast, stats,
SummarizedExperiment, utils, purrr, stringi, stringr, Matrix,
tidyr, jsonlite, readr, configr, DT, tools, fs, data.table,
htmltools, htmlwidgets, bsplus, shinyvalidate, shiny,
shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard,
biomaRt, callr, logr
Biobase, graphics, grDevices, methods, stats, tools, utils
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
grDevices, graphics, stats, utils, methods
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2,
gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer,
SingleCellExperiment, splines, stats, SummarizedExperiment,
utils
VariantAnnotation, MatrixGenerics, SummarizedExperiment,
data.table, stringr, httr, utils
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
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
data.tree, reshape2, networkD3, stringdist, purrr, ape,
cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap,
Biostrings, IRanges, BiocGenerics(>= 0.36.1), ggtree
methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD,
magrittr
Biobase, graphics, grDevices, methods, stats
ggplot2, class, concaveman, grid, BiocParallel,
spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors,
methods, spicyR, purrr, stats, data.table, dplyr, tidyr,
SingleCellExperiment, SpatialExperiment, SummarizedExperiment,
pheatmap
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
DelayedArray, GenomicRanges, HDF5Array, Matrix, stats,
stringr, utils
cBioPortalData, parallel, stringr, reshape2, data.table,
RColorBrewer, methods, LowMACAAnnotation, BiocParallel,
motifStack, Biostrings, httr, grid, gridBase, plyr
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
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
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, cluster, parallel, foreach,
doParallel, matrixcalc, Rtsne, corpcor, umap
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods
dplyr, rtracklayer, BSgenome, Biostrings, utils, methods,
IRanges, ExperimentHub
Biobase, graphics, grDevices, methods, stats, utils
robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony,
pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap,
logging, data.table, lmerTest, hash, optparse, grDevices,
stats, utils, glmmTMB, MASS, cplm, pscl, lme4
BiocParallel, DelayedArray, WGCNA, ff, data.table,
dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, RCurl,
RJSONIO, logging, methods, utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
utils, reticulate, S4Vectors, methods, basilisk,
ExperimentHub, AnnotationHub
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
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy
doParallel, igraph, bigstatsr, rjson, plyr, data.table,
UpSetR, reshape2, jsonlite, methods, ff, argparse, impute,
RnBeads.hg19, utils, stats
Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid,
reshape2, stats, utils, DOSE, clusterProfiler, pathview,
enrichplot, msigdbr, depmap
caret, parallel, doParallel, foreach, e1071, future.apply,
future, missForest, pcaMethods, tidyverse, stats, utils,
methods, SummarizedExperiment, S4Vectors
Biobase, affy, methods, stats, utils, zlibbioc
multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi,
methods, parmigene,igraph,reactome.db
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats,
utils, IRanges, methods, BiocGenerics, parallel, data.table
Biobase, graphics, grDevices, venn, mclust, stats, MASS
Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr,
stringr, abind, methods, parallel, reshape2, stats, stats4,
graphics, utils, SummarizedExperiment(>= 1.5.3), progress
methods, TFBSTools, IRanges, XVector, Biostrings
BiocGenerics, ProtGenerics, digest, irlba, biglm, utils
methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap,
rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva,
tibble, tidyr, vegan, stats, utils, Matrix
methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix,
BiocParallel
parallel, doParallel, psych, WGCNA, data.table, igraph,
visNetwork, cluster, clusterSim, methods, graphics, stats
Biobase, graphics, methods, utils, grDevices
stats, graphics, utils, limma (>= 3.30.13),
SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0),
BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData,
rmarkdown
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2,
graphics, grDevices, Gviz, IRanges, limma, methods, parallel,
S4Vectors, stats, SummarizedExperiment, utils
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges,
S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute,
Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA,
graphics, stats, utils, matrixStats
impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0),
grDevices, graphics, stats, utils, stringr, tibble, RPMM (>=
1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr
data.table, parallel, ROCR, matrixcalc, mclust, ggplot2,
doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm,
truncnorm, assertthat, BiocStyle, stats, utils
Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2,
ggseqlogo, magrittr, matrixStats, methods, patchwork, processx,
purrr, rlang, readr, stats, tools, tibble, tidyr, utils,
usethis, universalmotif (>= 1.9.3), xml2
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils,
AnnotationHub, MeSHDbi, yulab.utils
markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils,
fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite
methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
(>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
methods, mgcv, caret, S4Vectors, stats, utils, rlang,
graphics, matrixStats, tidyr
BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics,
methods, S4Vectors, Spectra (>= 1.7.2), BiocParallel,
SummarizedExperiment, QFeatures, graphics, CompoundDb
data.table, httr, jsonlite, methods, MultiAssayExperiment,
struct, SummarizedExperiment, utils
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75,
stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi,
MWASTools, mygene
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb,
GenomicFeatures, IRanges, ggplot2, Rsamtools, matrixStats,
purrr, data.table, magrittr, methods, utils, ensembldb,
EnsDb.Hsapiens.v86, stringr
rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges,
ggplot2, Rsamtools, purrr, data.table, methods, dplyr,
magrittr, reshape2
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench
Matrix, tools, robustbase, BiocGenerics, graphics, stats,
utils
grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4),
Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2),
gplots (>= 3.0.1), RColorBrewer (>= 1.1.2),
SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph,
dplyr, tidyr, tibble, ggplot2
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
ABSSeq, baySeq, Biobase, BiocGenerics, BiocParallel, biomaRt,
Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, gplots, graphics, grDevices, harmonicmeanp,
heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r,
magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel,
qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer,
S4Vectors, stats, stringr, SummarizedExperiment, survcomp,
utils, VennDiagram, vsn, yaml, zoo
epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan,
GenomeInfoDb, phyloseq, httr
methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot,
parallel, metafor, metap, rlang, topconfects, grDevices,
graphics, stats, htmlwidgets
methods, utils, stats, S4Vectors, bsseq, DSS, methylKit,
DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
methylKit, GenomicRanges, GenomeInfoDb, parallel,
BiocGenerics, S4Vectors, methods, stats, IRanges, msm
dplyr, plyr, GenomicRanges, SummarizedExperiment,
DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors,
sesameData, sesame, AnnotationHub, ExperimentHub, stringr,
readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges,
sfsmisc, progress, utils
rtracklayer, DelayedArray, HDF5Array, BSgenome,
DelayedMatrixStats, parallel, methods, ggplot2, matrixStats,
graphics, stats, utils, GenomicRanges, IRanges
Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase,
grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr,
minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter,
genefilter, methods, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute,
PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2,
ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra,
preprocessCore, dynamicTreeCut, planet
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, shiny,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors,
methods, parallel, ggplot2, gridExtra, rebus
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
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table,
GenomeInfoDb, S4Vectors
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
Rfast, grDevices, graphics, stats, utils, tools, methods,
shinyFiles, data.table, SummarizedExperiment
bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges,
GenomeInfoDb, GenomicRanges, methods, parallel, stats,
S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, Biobase, graphics, lattice, annotate,
genefilter, AnnotationDbi, minfi, stats4, illuminaio,
GenomicFeatures
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
methods, stats, utils, MASS, ape, decontam, vegan,
BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER,
BiocParallel, DelayedArray, DelayedMatrixStats, scuttle,
scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr
deSolve, stats, poweRlaw, gtools, S4Vectors, MatrixGenerics
methods, stats, S4Vectors, BiocGenerics, BiocParallel,
DelayedArray, scater, ggtree, ggnewscale, viridis, tibble,
tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape,
DirichletMultinomial
Biostrings, compositions, dplyr, reshape2, Rtsne, scales,
stats, tibble, tidyr, utils, vegan
graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply,
stats, phyloseq, metagenomeSeq, Biobase
shinyjs (>= 2.0.0), shinydashboard, shinycssloaders,
shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer,
dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0),
biomformat, tools, stringr, vegan, matrixStats, heatmaply, car,
broom, limma, reshape2, tibble, forcats, lubridate, methods,
plotly (>= 4.9.1)
dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2,
tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges,
tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR,
BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase,
ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest,
plotROC, vegan, pROC, BiocParallel
clusterProfiler (>= 4.0.2), config, DT, enrichplot, golem,
magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader,
htmltools, ggplot2, graphics, utils
ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang,
tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table
AnnotationDbi, Biobase, BiocParallel, compiler, data.table,
edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph,
graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma,
matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats,
utils, vegan
BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>=
1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba,
cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble,
matrixStats, ggraph, gtools, SummarizedExperiment, patchwork,
tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, Formula, data.table, pracma, MCMCpack, coda, modeest,
testthat, Rcpp, scales, dplyr, tidyr, rlang
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
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 (>= 0.15.16), HDF5Array, BiocParallel
methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>=
0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff,
foreach, matrixStats, lattice, data.table, grid, stats, utils
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
ggplot2, Biobase, stats, bsseq, methods
utils, methods, graphics, KernSmooth, stats
graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi,
Rgraphviz
methods, stats, utils, RCurl, httr, stringr, Hmisc, energy,
entropy, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db
DBI, RSQLite, stringr, sqldf, plyr, methods
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL,
NMF, biclust, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic,
Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero,
ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment,
GSEABase, org.Hs.eg.db, MatrixCorrelation, energy
corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats,
linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods,
methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod,
stringr, SummarizedExperiment
assertthat, caret, deldir, digest, distances, dplyr, filelock,
furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>=
2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble,
tidyr, tidyselect (>= 1.2.0), utils, withr
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r
reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
ggplot2
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats, magrittr,
SummarizedExperiment
AnnotationDbi, gplots, graphics, stats, utils
testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma,
Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq,
xtable
ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation,
BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb,
GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools,
magrittr, methods, grDevices, graphics, stats, utils, stringr,
data.table
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr,
stringr, cowplot, utils, stats, grDevices
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071, ggplot2, wesanderson
S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics,
methods, grDevices, reshape2, NMI, zoo, ClusterR, splines,
matrixStats
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk, stringi
stats, utils, RCy3, stringr, graphics, grDevices, RUnit,
BiocParallel, igraph
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics,
grid, grDevices, magrittr, methods, MKmisc,
MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr,
reshape2, rlang, stats, stringr, tibble, tidyr, utils
methods, stats, utils, grDevices, graphics, BiocGenerics,
GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome,
glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid,
circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb,
tools, vioplot
parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>=
0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>=
2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>=
0.1.9), limma, tibble, dplyr, qlcMatrix, pheatmap, stringr,
proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>=
0.12.0)
parmigene, randomForest, SummarizedExperiment, gplots,
circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase,
limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats,
RISmed, grid, utils
MASS, splines, lattice, IRanges, GenomicRanges,
GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi,
lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble,
tidyr, ggplot2, Biobase, IRanges, S4Vectors
S4Vectors, stats, utils, methods, grDevices, graphics,
BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges,
GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools
methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors
(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings,
BSgenome, rtracklayer, VariantAnnotation, BiocParallel,
motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets,
stats, stats4, utils, XML, TFBSTools
httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales,
gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb,
methods, biomaRt, stats, IRanges
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra,
utils, stringr, ggpubr, stats, cowplot, RColorBrewer, tidyr,
scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr,
rmarkdown, ggrepel, gghalves, tools
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel,
dplyr, foreach, methods, parallel, rlang, seqinr, stringr,
tibble, tidyr, stats, stringi
BiocParallel, S4Vectors, IRanges, methods, ProtGenerics,
MsCoreUtils, DBI, utils
BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats
MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.3.6), utils,
BiocParallel
methods, S4Vectors, IRanges, Spectra, SummarizedExperiment,
QFeatures
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
BSgenome, easyRNASeq, edgeR, GenomicAlignments,
GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges,
parallel, plyr, Rsamtools, R.utils, stats,
SummarizedExperiment, S4Vectors, utils
softImpute, methods, stats, graphics, pdist, reticulate,
scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr,
dplyr
doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC,
randomForest, RankProd, stats, utils
MsCoreUtils, BiocParallel, IRanges (>= 2.13.28), plyr, vsn,
grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16),
mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS,
Rcpp
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests,
ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang,
stringr, tibble, AnnotationHub, AnnotationDbi, xtable
SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), crmn,
preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2),
magrittr, rlang, stats, stringr, methods, missForest, sva, VIM,
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, MultiAssayExperiment, codetools
MSstatsConvert, data.table, checkmate, MASS, limma, lme4,
preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, marray, stats, grDevices, graphics, methods, statmod
data.table, log4r, methods, checkmate, utils, stringi
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
ggplot2, BiocParallel, caret, gridExtra, reshape2, stats,
utils, grDevices, graphics, MSstats
shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,
data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
MSstatsConvert, gplots, marray, DT, ggrepel, uuid, utils,
stats, htmltools, methods, tidyr, grDevices, graphics
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate
methods, stats, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, DelayedArray
graphics, grDevices, stats, methods, fields
methods, GenomicRanges (>= 1.25.93), BiocBaseUtils,
BiocGenerics, DelayedArray, S4Vectors (>= 0.23.19), IRanges,
Biobase, stats, tidyr, utils
Matrix, ggplot2, MultiAssayExperiment, ropls, graphics,
methods, plotrix, grDevices, pcaMethods
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek,
data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges,
ggplot2, grid, karyoploteR, magrittr, methods, parallel,
plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi,
tidyr, tidyselect, utils
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman,
limma
magrittr, graphite, AnnotationDbi, dplyr, fgsea, metap,
rappdirs, rlang, methods
data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman,
pheatmap, methods, GenomicRanges, graphics, stats, utils,
pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, parallel, doParallel, foreach, grDevices, graphics,
utils, SummarizedExperiment, stats
golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr,
anyLib, caret, biosigner, mixOmics, stats, DESeq2,
clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor,
metap, infotheo, igraph, networkD3, easyPubMed, utils,
htmltools, rmarkdown, ggnewscale
stats, utils, methods, igraph, Matrix, BiocGenerics,
BiocParallel, IRanges, S4Vectors, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, BiocNeighbors,
BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran,
batchelor, uwot
magrittr, data.table, utils, R.utils, dplyr, stats,
GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings,
stringr, VariantAnnotation, googleAuthR, httr, jsonlite,
methods, parallel, rtracklayer, RCurl
BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr,
edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest,
lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors,
scales, scater, scuttle, sctransform, stats,
SingleCellExperiment, SummarizedExperiment, variancePartition,
viridis
SummarizedExperiment, VariantAnnotation, cowplot, Biostrings,
base, methods, magrittr, tibble, tidyr, gtools, gridExtra,
MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang,
BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges,
IRanges, S4Vectors, uwot, ggplot2, stringr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig,
topicmodels, ggrepel, withr, plotly, utils, factoextra,
cluster, ComplexHeatmap, philentropy, shinydashboard, sortable,
maftools, shiny, shinyjs, shinyalert, shinybusy, shinyBS,
TCGAbiolinks, shinyjqui, stringi
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf,
plyr
httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
graphics, methods, baseline, signal, GenomicAlignments,
GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils,
Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot,
csaw
cpp11 (>= 0.2.5), readr, S4Vectors, SummarizedExperiment,
BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp,
dplyr, data.table, e1071, fs, GenomicRanges, ggrastr, glue,
graphics, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils,
RSQLite, Rsamtools, scales (>= 1.2.0), scico, stats, stringr,
tibble, tidyr, utils, withr, zlibbioc
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats,
rlang, stringr, knitr, testthat, utils, AnnotationDbi, httr,
GenomicRanges, tidyverse, VarfromPDB, org.Hs.eg.db, curl,
dplyr, XML, XML2R
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2
graph, KEGGgraph, methods, RBGL, RCy3, R.methodsS3
httr, xml2, utils, methods, grDevices, ggplot2, IRanges,
GenomicRanges, S4Vectors
R.utils, matrixStats, plyranges, transport, Rsamtools,
S4Vectors, grDevices, graphics, rtracklayer, dplyr,
GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots,
BiocGenerics, rlang
Seurat, SingleCellExperiment, SummarizedExperiment, ks,
Matrix, stats, methods
e1071, nnet, randomForest, naturalsort, graphics, stats,
utils, matrixStats, epiNEM
airway, DelayedArray, DelayedMatrixStats, DESeq2, methods,
methods, NetActivityData, SummarizedExperiment, utils
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
R.utils
RColorBrewer, DT, stats, clusterProfiler, data.table, gplots,
jsonlite, plyr
ROCR,pracma,ggplot2,glmnet,igraph,reshape2,
parallel,stats,utils,MultiAssayExperiment,graphics,grDevices,
methods,BiocFileCache,GenomicRanges,
bigmemory,doParallel,foreach,
combinat,rappdirs,GenomeInfoDb,S4Vectors,
IRanges,RColorBrewer,Rtsne,httr,plotrix
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr,
AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods,
stats
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer
entropy, SummarizedExperiment, SingleCellExperiment, Matrix,
cluster, data.table, stats, methods, DelayedArray, HDF5Array
(>= 1.15.13)
RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi,
matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet,
data.table, vegan, stats, utils, reshape, reshape2, penalized,
parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS,
assertthat, tidyr, methods, dplyr, graphics
methods, SingleCellExperiment, parallel, irlba, Matrix,
DelayedArray, BiocSingular, SharedObject, stats
Biostrings, checkmate, dplyr (>= 1.0.0), DT, forcats,
ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate,
methods, pander, plotly (>= 4.9.4), readr, reshape2, rlang,
rmarkdown, scales, stats, stringr, tidyr, tidyselect (>=
0.2.3), utils, zoo
graphics, grDevices, marray, methods, nnet, stats
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
BRISC, BiocParallel, Matrix, matrixStats, stats, methods
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb,
S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl,
dbplyr,utils,ggplot2,igraph,stats,reshape2,readr,
GO.db,zlibbioc,
biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment,
matrixStats, ggforce
methods, stats, utils, grDevices, parallel, GenomeInfoDb,
GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2),
bamsignals (>= 1.4), rtracklayer (>= 1.32)
dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr,
stats, methods
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
Biobase, BiocGenerics, Biostrings, GenomeInfoDb,
GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr,
ggplot2, magrittr, parallel, stats, utils, grDevices
stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang,
S4Vectors, scales, InteractionSet, ggplot2, grDevices,
plyranges, ks, speedglm, data.table, progress, ggridges
methods, stats, utils, tools, parallel, magrittr, Rcpp (>=
1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache,
BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray,
DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges,
HDF5Array, IRanges, plotly, R.utils, rhdf5, rtracklayer,
SummarizedExperiment, S4Vectors
multtest (>= 1.7.3), graphics, grDevices, stats, interp
EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2,
grDevices, utils
BiocGenerics, BiocFileCache, dasper, derfinder, dplyr,
IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel,
magrittr, rtracklayer, S4Vectors, stringr, data.table,
megadepth, methods, plyr, purrr, tibble, utils
GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz,
IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny,
shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr
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
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), foreach, BiocManager, utils, S4Vectors (>= 0.9.25),
RSQLite, DBI, ff
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
compositions, DT, grDevices, knitr, jsonlite, matrixStats,
rmarkdown, shiny, stats, vegan, zCompositions
stats, utils, grDevices, graphics, methods, rexposome, limma,
sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet,
SmartSVA, isva, parallel, SummarizedExperiment, stringr
SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2,
BiocParallel, parallel, grDevices, graphics, stats, utils,
methods, BiocGenerics
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
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
survminer, survival, fastmatch, reshape2, stringr, beeswarm,
grDevices, DT, shiny, shinythemes, shinyWidgets, plotly,
networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea,
openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics,
grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2,
S4Vectors, SummarizedExperiment, RSQLite, Matrix,
shinycssloaders
dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr,
tidyselect, grid, stats, stringr
checkmate, crayon, curl, digest, dplyr, httr, igraph,
jsonlite, later, logger, magrittr, progress, purrr, rappdirs,
readr(>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats,
stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2,
yaml
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, stringr
Rtsne, plotly, gplots, grDevices, graphics, stats, utils,
methods, flowCore
Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
igraph, AnnotationHub, SummarizedExperiment
methods,Biobase,BiocGenerics,flowCore(>=
1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>=
3.99.1),flowClust(>= 3.11.4),RBGL,graph,data.table,RColorBrewer
MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist,
summarytools, graphics, stats, utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl
limma, stats, reshape, ggplot2, grDevices, RColorBrewer,
pheatmap, knitr, methods, devtools, parallelDist,
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table,
stringr, randomForest, xfun, stats, utils, parallel, graphics
AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt,
biomartr, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0),
BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2
(>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5),
GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>=
2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils,
Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>=
1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>=
0.21.3), tools, utils, xml2 (>= 1.2.0)
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils,
BiocFileCache, DBI, dbplyr, tibble
Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph,
IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, grr, repmis, ggtree, tools
BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics,
GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap,
graphics, IRanges, matrixStats, plotly, plyr, pcaMethods,
PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines,
stats, utils
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
Biostrings, GenomicRanges, kmer, ape, methods, IRanges,
S4Vectors
FactoMineR, MultiAssayExperiment, methods, graphics, stats,
utils
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGGREST, nlme
GenomicRanges, igraph, motifmatchr, stats, utils, grDevices,
graphics
SummarizedExperiment, S4Vectors, stats, methods, abind,
BiocParallel
SummarizedExperiment, KEGGREST, igraph, data.table, methods,
stats, magrittr, CompQuadForm, tibble
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb,
grDevices
clusterProfiler, dplyr, forcats, GSEABase, igraph, limma,
metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer,
rlang, tibble, withr, utils
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
tidyr, stringr, dplyr, tibble, magrittr, futile.logger, utils,
easycsv, rentrez, igraph, RColorBrewer, data.table, colorspace,
grDevices, rlang, methods
stats, tidyr, purrr, furrr, tibble, glue, tidygraph, igraph,
proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress,
Matrix, matrixLaplacian, keras, nloptr, shadowtext, methods,
DOSE, stringr, reticulate
stats, utils, dplyr, rlang, iterators, parallel, foreach,
doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges,
S4Vectors
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
EMT, mclust, Matching, data.table, stats, grDevices, graphics,
utils
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
org.Hs.eg.db, KEGGREST, methods, utils
lars, methods, parallel, stats, survival, utils
utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr,
rappdirs
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly,
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
lattice, grDevices, cowplot, methods, reshape2, stats, Matrix,
DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel,
Rcpp, dqrng
data.table, MultiAssayExperiment, ConsensusClusterPlus,
igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro,
CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics,
survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel,
rlang, piano, scales, survcomp, genefu, ggplot2, switchBox,
reportROC, pROC, verification, utils
circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2,
grDevices, grid, gridExtra, methods, plyr, stats, utils
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
assertthat, circular, conicfit, doParallel, foreach, genlasso
(>= 1.4), graphics, methods, parallel, scater,
SingleCellExperiment, SummarizedExperiment, stats, utils
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo,
ggplot2, methods, parallel, cowplot
graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr,
tidyr, magrittr, stats, methods, utils
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, pheatmap, scales, ccaPP, grid,
grDevices, AnnotationDbi, DESeq2, data.table, curl
BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, magicaxis,
RColorBrewer, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
checkmate, boot, coop
SingleCellExperiment, RColorBrewer, igraph, transport, pracma,
cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap,
scatterplot3d, VGAM, methods, grDevices, graphics, stats,
utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment,
Biobase, phateR, reticulate
igraph, Matrix, foreach, doParallel, dplyr, stats, utils,
parallel
Biobase, biodb, biodbChebi, data.table, futile.logger,
ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets,
igraph, limma, methods, MultiAssayExperiment, MultiDataSet,
PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble,
tidyr, utils, VennDiagram
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, gplots, Category, AnnotationDbi, hopach,
biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
hgu133a.db, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
ape, phangorn, tidyr, ggplot2, ggtree, methods
BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges,
S4Vectors, edgeR, cli, utils
plyr, stats, graphics, matrixStats, methods
ruv, e1071, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils,
SummarizedExperiment, methods, S4Vectors, BiocGenerics,
ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply,
RColorBrewer, RCurl, shiny, shinyBS, shinyFiles, shinyjs,
OmaDB, plyr, xml2, zoo, yaml
Matrix, GenomicRanges, GenomeInfoDb, supraHex, scales,
grDevices, ggrepel, ROCR, randomForest, glmnet, lattice, caret,
plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr,
tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
utils, stats, graphics, grDevices, methods, IRanges,
GenomicRanges, Rsamtools, GenomicAlignments
bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit,
Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices,
graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr,
gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI,
DOSE
methods, PICS, graphics, grDevices, stats, Gviz, fda,
BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges,
S4Vectors
BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment,
SummarizedExperiment, Seurat, matrixStats, Matrix, cluster,
aricode, methods, utils, dplyr, grid, scales, scran,
viridisLite, clue, randomcoloR, ggplot2, cowplot,
intrinsicDimension, scater, knitr, reshape2, stats, Rtsne,
uwot, circlize, RColorBrewer
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
GenomeInfoDb, parallel, stats, utils, rmarkdown
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
utils, Biobase (>= 2.5.5), MASS, methods
curl, data.table, dplyr, grDevices, grid, ggplotify, IRanges,
methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats,
strawr, tools, utils
methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>=
1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb,
Rsamtools, S4Vectors (>= 0.23.10), utils
stats, impute, pcaMethods, missForest, ggplot2, methods,
SummarizedExperiment, S4Vectors, matrixStats, grDevices,
reshape2, utils
ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT,
LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils,
Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges,
Biostrings, BSgenome (>= 1.32.0)
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma,
zlibbioc
broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, ggplot2,
ggrepel, glasso (>= 1.11), glmnet, impute, limma, magrittr,
mixOmics, randomForest, RankProd (>= 3.14), rmarkdown,
SummarizedExperiment, tibble, tidyr, uwot, vegan
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
pheatmap, ggplot2, RColorBrewer, grDevices,
SummarizedExperiment, limma
methods, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>=
2.0.0), tibble, dplyr, magrittr, purrr, future, furrr, tidyr
(>= 0.8.3.9000), lifecycle, ggplot2, foreach, tidybayes, edgeR,
benchmarkme, parallel, rlang, stats, utils, graphics
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
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)
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, GenomeInfoDb, S4Vectors
S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics,
e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW,
foreach, pbapply, stats, parallel, gtools, rCGH
AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2,
IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang,
scales, S4Vectors, SummarizedExperiment, stats, tibble
Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2,
grDevices, lazyeval, lubridate, magrittr, pheatmap,
preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang,
scales, stats, sva, tidyr, tibble, tools, utils, viridis,
wesanderson, WGCNA
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
stats, graphics, utils, grDevices, methods, pracma, Biobase,
minpack.lm, BiocParallel, missForest, ropls
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, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid,
circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices,
rlang, tiff, Rsamtools
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra,
decoupleR, reshape2
methods, cluster, stats, limma, CoGAPS, NMF, ROCR, ggalluvial,
RColorBrewer, dplyr, reshape2, viridis, scales, ggplot2
stats4, 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
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker,
shinyhelper, shinyWidgets, shinyjs, colorspace, stats,
grDevices, grid, BiocGenerics, shinydashboard
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.30.5), DAPARdata (>= 1.28.0), rhandsontable,
data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets,
webshot, shinythemes, later, shinycssloaders, future, promises,
shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot
data.table, stringr, ensembldb, AnnotationFilter,
EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v79,
Rcpi, methods, utils
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, cluster,
colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR,
fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices,
highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma,
pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast,
R.utils, reshape2, shinyjs, stringr, stats,
SummarizedExperiment, survival, tools, utils, XML, xtable,
methods
utils, stats, igraph, methods, Matrix, BiocParallel,
BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db
Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
utils
Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
S4Vectors, data.table, grDevices, graphics, stats, utils,
SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools,
Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2,
gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5,
Matrix
biovizBase, Biostrings, GenomicRanges, IRanges, data.table,
methods
data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots,
Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub,
GenomicRanges, graph, grDevices, stats, utils
doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2,
parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter,
stats, grDevices, methods, utils, graphics, pwrEWAS.data
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang,
RSeqAn
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
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 (>=
0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply
(>= 1.8.1)
methods, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.27.1),
AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.7.2),
igraph, plotly
rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils,
stats, igraph, VIM, scales, grDevices, graphics
methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph
(>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0),
ggdendro, ggplot2, graphics, grDevices, IRanges, limma,
magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang,
scales, stats, stringr, tibble, tidyr, tidyselect, utils
reshape, ggplot2, Biostrings, biovizBase, graphics, methods,
plyr, stats
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
Biobase, limSolve, MASS, methods, preprocessCore, stats,
SummarizedExperiment, ggplot2, tidyr, rlang, utils
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, stats, tools,
BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings,
BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, ShortRead,
BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles,
AnnotationDbi
methods, parallel, ggplot2, pheatmap, clValid, igraph,
data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors,
IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
ggbio
methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
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)
SummarizedExperiment, BiocGenerics, data.table, S4Vectors,
Biobase, parallel, BiocParallel, RColorBrewer, caTools,
magicaxis, methods, reshape2, scales, grDevices, graphics,
stats, utils, assertthat, matrixStats, downloader
BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics,
methods, S4Vectors, stats, SummarizedExperiment, utils
IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist,
matrixStats, S4Vectors
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
methods, graphics, utils, stats, Rdpack (>= 0.7)
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools,
BSgenome, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
SummarizedExperiment, GenomicScores
Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach,
grDevices, stats, utils
utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors (>=
0.23.19), IRanges, GenomeInfoDb, GenomicAlignments
GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer,
GenomicFeatures, rmarkdown (>= 0.9.5), genomation (>= 1.5.5),
knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply,
RSQLite, proxy, pheatmap, ggplot2, cowplot, ggseqlogo, utils,
ranger, gprofiler2
stringr, gplots, ggplot2, methods, stats, utils, shiny
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
AUCell (>= 1.1.6), BiocGenerics, data.table, graphics,
GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble,
GSEABase, methods, R.utils, stats, SummarizedExperiment,
S4Vectors, utils
RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
grDevices, graphics, methods
stats, utils, methods, RCurl, rjson, foreach, doParallel,
Biostrings, GOSemSim, rcdk (>= 3.3.8)
RcppAnnoy, igraph, NbClust, Rtsne, ggplot2, methods, pracma,
umap, grDevices, graphics, stats
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools, basilisk
rappdirs, methods, utils, git2r, httr, S4Vectors
httr, methods, RJSONIO, XML, utils, BiocGenerics, stats,
graph, fs, uuid, uchardet, glue, RCurl, base64url, base64enc,
IRkernel, IRdisplay, RColorBrewer, gplots
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
httr, jsonlite, utils, magick (>= 2.5.1), data.table,
doParallel, foreach, parallel
neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table,
rlang, ReactomeContentService4R, doParallel, parallel, foreach
jsonlite, httr, progress, ggplot2, methods, gplots,
RColorBrewer, dplyr, tidyr
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>=
3.3.5), ggraph, reactome.db, igraph, graphite, gson
utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends,
dir.expiry, filelock, BiocStyle
dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
phyloseq, ks, reshape2, ggplot2, stats, methods, graphics,
grDevices, matrixStats, Matrix
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocFileCache, methods, rtracklayer, S4Vectors, utils, RCurl,
data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools
minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl,
R.utils, BiocFileCache, basilisk, reticulate,
DelayedMatrixStats
BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb,
GenomicFeatures, graphics, grDevices, httr, IRanges, methods,
parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats,
stringr, utils
AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils
randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA,
ggplot2 (>= 2.2.0), methods, reshape2, magrittr
memoise, GenomicRanges, IRanges, BSgenome, Biostrings,
rtracklayer, parallel, graphics, stats, utils, methods,
GenomeInfoDb, S4Vectors, tools
stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2,
methods, scales, cluster, grid, grDevices
BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats,
DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6),
knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>=
0.9.5), S4Vectors, SummarizedExperiment, utils
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges,
Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils,
BiocFileCache
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
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, Rsolnp,
cluster
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
rJava, graphics, stats, utils, grDevices
Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet,
ggplot2, gridExtra, IRanges, lsa, nnls, parallel, reshape2
utils, stats, methods, S4Vectors, Biobase,reshape2,
AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1),
magrittr, bigrquery, ExperimentHub, AnnotationHub, rlang
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
httr, stringi, rsvg, magick, data.table, Biostrings, utils,
rvest, xml2, IRanges, S4Vectors
utils, GenomeInfoDb, data.table, IRanges, GenomicRanges,
parallel, Rsamtools
Biostrings, GenomicRanges, methods, graphics, seqLogo
httr, rJava, GenomicRanges, rtracklayer, data.table, utils,
plyr, xml2, methods, S4Vectors, dplyr, stats, glue,
BiocGenerics
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2,
graphics, IRanges, methods, regioneR, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene
graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats,
GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db,
progress, circlize, AnnotationDbi,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer,
S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
AnnotationDbi
GenomicFeatures, SGSeq, GenomicRanges, methods, utils
BiocGenerics, BiocParallel, Biostrings, data.table, dplyr,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges,
plotly, rlang
Rcpp (>= 1.0.2), graphics, stats, data.table, elitism,
methods, S4Vectors, IRanges, GenomicRanges, matrixStats,
reldist, doParallel, foreach, parallel, qvalue, DESeq2,
ggplot2, BiocFileCache,BiocGenerics
BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2,
GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments,
ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo
AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq,
GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges,
methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread,
S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils,
cluster, stats, graphics, grid
car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2,
graphics, grDevices, grid, methods, nls2, nnet, rlang,
S4Vectors, scales, stats, stringr, SummarizedExperiment,
tibble, rtracklayer, reshape2, utils
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4
graphics, methods, stats, utils, grid, gridExtra, reshape2,
gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL,
linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph,
BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb,
AnnotationFilter, EnsDb.Hsapiens.v86
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb,
S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
grDevices
dplyr, ggplot2, RColorBrewer, grid, regioneR, valr,
caretEnsemble, GenomicFeatures, rtracklayer, GenomicRanges,
GenomeInfoDb, ComplexHeatmap, AnnotationHub, VennDiagram,
callr, circlize, ggplotify, ggprism, methods, stats, RLHub,
aws.s3, pheatmap
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges,
SummarizedExperiment, devtools, TBX20BamSubset,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2,
BiocStyle
processx, BiocManager, rtracklayer, stats, tools, methods,
GenomicRanges, stringr
ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats,
SummarizedExperiment, methods
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb,
bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot
RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid,
hwriter, lattice, latticeExtra, limma, methods, splots (>=
1.13.12), abind, locfit, Biobase
methods, stats, grDevices, matrixStats, BiocGenerics,
Biostrings (>= 2.57.2), BiocParallel, GenomicFeatures,
GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools,
BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0),
reshape2, graphics, ROCR
methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
stats, ranger
methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
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
biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices,
graphics, stats, Rcpp (>=
0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
SummarizedExperiment, GenomicAlignments (>= 0.99.4),
rtracklayer, GenomeInfoDb
stats, methods, ROTS, matrixStats, foreach, parallel,
doParallel, doRNG, rngtools, SummarizedExperiment, nlme,
qvalue, grDevices, graphics, utils
httr, progress, jsonlite, utils, Biobase, BiocGenerics (>=
0.23.1)
Biobase, ggplot2, graphics, grDevices, methods, plotly, stats,
MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils
Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods,
patchwork, reshape2, S4Vectors, shiny, shinycssloaders,
shinyFeedback
BiocFileCache, jsonlite, xml2, RCurl, curl, utils
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
GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel,
treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods,
umap
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,
BiocParallel, stats
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, RCurl, assertthat, stringi, rvest, data.table, xml2,
dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis,
knitr, scales, rmarkdown, htmltools
BiocGenerics, data.table, DelayedArray, GenomicRanges,
GenomeInfoDb, grDevices, httr, limma, methods,
RaggedExperiment, RCircos, RCurl, RJSONIO, rvest, S4Vectors (>=
0.23.10), stats, stringr, SummarizedExperiment, survival,
TCGAutils (>= 1.9.4), utils, XML
RedeR, minet, viper, mixtools, snow, stats, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr,
pheatmap, grDevices, graphics, utils
survival, RColorBrewer, grDevices, graphics, stats, utils,
scales, data.table, egg, ggplot2, pheatmap, dunn.test
Biobase, methods, ggplot2, pROC, fdrtool, splines, utils,
tibble
shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils
httr, utils, XML, rjson, data.table, tidyr, RCurl
methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0)
rJava, Biostrings, IRanges, utils, stats, cluster, binom
locfdr, SummarizedExperiment, BiocParallel, limma, pbapply,
ggplot2, boot, Matrix, stats, methods, graphics
methods, reshape2, scales, gridExtra, XML
Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph,
rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr,
KEGGREST, bookdown
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
Biostrings, GenomicRanges, IRanges, data.table, BiocParallel,
methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi,
utils, graphics, grid, ggseqlogo, cowplot
AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel,
Biostrings, data.table, digest, DT, ensembldb, fst,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2,
htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs,
rtracklayer, S4Vectors, scanMiR, scanMiRData, shiny,
shinycssloaders, shinydashboard, shinyjqui, stats, utils,
waiter
dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats,
e1071, ape, kernlab, AnnotationHub, utils
BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment,
SingleCellExperiment, DelayedMatrixStats
stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics,
S4Vectors, SummarizedExperiment, DelayedArray,
DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular,
BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer,
RcppML, uwot, pheatmap, ggrastr, ggrepel
grid, ggplot2, plyr, spatstat.geom, stats, grDevices
SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods,
Matrix
reshape2, future, future.apply, ape, scales, Seurat, ggplot2,
ggtree, patchwork, methods, stats, base, utils
SingleCellExperiment, SummarizedExperiment, Matrix, methods,
utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel,
iterators, foreach, Seurat
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo
methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools
(>= 2.1.1), rstan (>= 2.18.1), SeuratObject,
SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr,
rlang, tibble, boot, lifecycle, stats, tidyselect, utils,
ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr,
glue
ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales,
RColorBrewer, corrplot, stats, grDevices, graphics, utils,
MASS, matrixStats, methods
igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors,
BiocSingular, S4Vectors, SummarizedExperiment, scran, scater,
scuttle, bluster, methods, DelayedArray, xgboost, stats, utils,
MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools,
rtracklayer
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SingleCellExperiment, SummarizedExperiment, grDevices,
graphics, stats, S4Vectors, scran
Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq,
BiocParallel, mclust, SingleCellExperiment, cluster, Oscope,
SummarizedExperiment, stats, methods
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
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats, dplyr, pROC
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1),
fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel,
grDevices, graphics, stats, utils, DESeq2, locfit
hexbin, stats, methods, cluster, dplyr, entropy, ggforce,
scales, grid, concaveman
S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix,
SummarizedExperiment, IRanges, methods, stats, BiocParallel,
reshape, ggplot2, igraph, grDevices, ggforce, graphics
dplyr, rmarkdown, data.table, Biostrings, parallel, stats,
plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR,
kableExtra, tibble, scales, rlang, flowCore, methods
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
BiocParallel, BiocSingular, cluster, DelayedArray,
DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel,
pdist, proxy, ruv, S4Vectors (>= 0.23.19), SingleCellExperiment
(>= 1.7.3), SummarizedExperiment
methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>=
2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS,
logitnorm, ggplot2, matrixStats, assertthat, viridis, coda,
BiocStyle, cowplot, stats, SummarizedExperiment,
SingleCellExperiment, Matrix, dplyr, S4Vectors
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)
SingleCellExperiment, SummarizedExperiment, stats, methods,
graphics, grDevices, parallel, quantreg, cluster, moments,
data.table, BiocParallel, S4Vectors, ggplot2, forcats,
BiocGenerics
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, edgeR, fpc, gplots, grDevices,
hexbin, limma, matrixStats, mixtools, RColorBrewer, boot,
rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
stats, grDevices, graphics, utils, DescTools, RColorBrewer,
gplots, foreach, parallel, doParallel, DNAcopy, BSgenome,
Biostrings, BiocGenerics, S4Vectors
Biostrings, methods, snpStats, VariantAnnotation,
GenomicRanges, BiocParallel, graphics, SummarizedExperiment
methods, stats, utils, SingleCellExperiment,
SummarizedExperiment, MultiAssayExperiment, MsCoreUtils,
matrixStats, S4Vectors, dplyr, magrittr
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix,
DelayedArray, ScaledMatrix, MatrixGenerics
AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings,
data.table, dplyr, DropletUtils, flexmix, GenomicRanges,
GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices,
graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0),
mclust, methods, MultiAssayExperiment, org.Hs.eg.db,
org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate,
Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer,
SummarizedExperiment, S4Vectors, scales, stats, stringr,
tibble, tidyr, tools, utils,
SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel,
Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph,
statmod, DelayedArray, DelayedMatrixStats, BiocSingular,
bluster, metapod, dqrng, beachmat
randomForest, e1071, stats, SummarizedExperiment,
SingleCellExperiment, methods
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), BiocParallel (>=
1.12.0)
stringdist, dplyr, reshape2, ggalluvial, stringr, vegan,
powerTCR, SingleCellExperiment, SummarizedExperiment, plyr,
parallel, doParallel, methods, utils, rlang, igraph, ggraph,
tidygraph, SeuratObject
data.table, GenomicAlignments, GenomicFeatures, GenomicRanges,
Rsamtools, ShortRead, parallel, plyr, BiocGenerics,
BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods,
ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio,
rtracklayer, SingleCellExperiment, SummarizedExperiment,
Rsubread
DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix,
SingleCellExperiment, SummarizedExperiment, BiocSingular
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
methods, RSQLite, igraph, S4Vectors, plotly, reactome.db,
AnnotationDbi, SummarizedExperiment, SingleCellExperiment,
nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8),
abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle,
knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics,
stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats,
ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork,
schex, ggplot2
GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly,
tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr,
S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor,
methods, scales, msigdbr, schex, tibble, ggplot2, igraph
BiocParallel, Rtsne, grDevices, graphics, stats
data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph,
clustree, scran, sys, epivizrData, epivizrServer, ggraph,
scater, Seurat, SingleCellExperiment, ggplot2, stats, utils
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment,
DelayedArray, DelayedMatrixStats, beachmat
S4Vectors, SummarizedExperiment, seriation, ComplexHeatmap,
circlize, methods, randomcoloR, stats, grid, grDevices,
matrixStats
ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges,
S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils,
methods, chromhmmData
Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils,
abind
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods,
stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2
(>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings,
grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1)
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>=
2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods,
rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2),
stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils
ggplot2, grid, igraph, utils, yulab.utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, ggplotify, grDevices, grid, IRanges, limma,
methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools,
rtracklayer, S4Vectors, stats, UpSetR
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, Biobase, BiocGenerics,
gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW,
logistf, Matrix, data.table,
graphics, BiocParallel, utils, methods, stringr, readr,
tibble, illuminaio, MASS, wheatmap (>= 0.2.0), GenomicRanges,
IRanges, grid, preprocessCore, S4Vectors, ggplot2,
BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment,
dplyr, reshape2
BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR,
openxlsx, pheatmap, stats, circlize, methods, sva
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>=
2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>=
1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19),
grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7),
stats
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter,
methods, zlibbioc, lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC,
RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot, lmerTest, mlr3learners, mlr3tuning,
paradox, lgr
biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer,
Matrix, SparseM, graphics, stats, utils, SummarizedExperiment,
BiocParallel, methods
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5,
GSEABase, DelayedArray, BiocGenerics, tibble
BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb,
GenomicRanges, IRanges, nloptr, methods, stats, utils,
PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat,
survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071,
randomForest, ada, future.apply, ggplot2, pROC, pheatmap,
RColorBrewer, listenv, reshape2, scales, survminer, dplyr,
ggpubr, cowplot, tibble, readr, shiny, shinydashboard,
shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr,
BiocFileCache, proxy, rtracklayer, BSgenome
ggplot2, org.Hs.eg.db, patchwork, AnnotationDbi, BiocGenerics,
ComplexHeatmap, DGEobj.utils, GSVA, IRanges,
SummarizedExperiment, consensusOV, dplyr, ensembldb, ggridges,
grid, magrittr, matrixStats, maxstat, methods, openair,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, stats, survival, survminer,
viridis
quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0),
VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb,
GenomicRanges, rtracklayer, SummarizedExperiment, graphics,
stats, utils
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
basilisk, BiocParallel, data.table, dplyr, ggplot2, tools,
Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer,
RCurl, reticulate, sparseMatrixStats, SummarizedExperiment,
tidyr
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors,
grDevices, SummarizedExperiment, methods, cytomapper
GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong,
digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods,
clue, grDevices, graphics, stats, utils, proxyC, Matrix,
cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0)
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
Biostrings, BiocGenerics, dplyr, GenomicAlignments,IRanges,
methods, reshape2, rlang, Rsamtools, stats, stringr, tidyr,
utils
methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges,
DelayedArray
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics,
stringr, foreach, multtest, scran, utils,
ape, AnnotationHub, batchelor, BiocParallel, celldex,
colourpicker, colorspace, cowplot, cluster, ComplexHeatmap,
data.table, DelayedMatrixStats, DESeq2, dplyr, DT,
ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel,
ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, igraph,
KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr,
multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge
(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR,
SoupX, sva, reshape2, shinyalert, circlize, enrichR, celda,
shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>=
1.14), tools, tximport, fishpond, withr, GSEABase, R.utils,
zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown,
magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang,
TSCAN, TrajectoryUtils, scuttle, utils, stats
BiocGenerics, Biostrings, BSgenome, GenomeInfoDb,
GenomicRanges, data.table, grDevices, plyr, IRanges,
RColorBrewer, stats, QuasR
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat,
parallel
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb,
GenomicFeatures, GenomicRanges, IRanges, methods, parallel,
Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
minfi, S4Vectors (>= 0.19.1), RColorBrewer
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
graphics, grDevices, igraph, matrixStats, methods, S4Vectors,
SingleCellExperiment, SummarizedExperiment
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2,
reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph,
Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics,
stats, utils
aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
R6, httr, rlang, purrr, jsonlite, assertthat, data.table,
Matrix, magrittr, methods, stringr, stats, IRanges,
GenomicRanges, SummarizedExperiment
basilisk, reticulate, irlba, stats, assertthat
DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel,
VariantAnnotation, BiocGenerics, IRanges, methods,
SummarizedExperiment, RColorBrewer, Biostrings, grDevices,
gridExtra, stats, grid, utils, reshape2, scales, S4Vectors
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb,
GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
rtracklayer, preprocessCore, chipseq, BiocParallel
S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio,
reshape2, NMF, pcaMethods, Biobase, methods, proxy
Seurat, SingleCellExperiment, SummarizedExperiment, dplyr,
methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg,
magrittr, utils, S4Vectors, DropletUtils, jsonlite, png
babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet,
checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>=
1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>=
2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix,
methods, plotly (>= 4.9.0), stats, utils, viridis
stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2,
gridExtra, reshape2
ggplot2, methods, stats, dplyr, spatstat.geom,
spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
reticulate, basilisk (>= 1.9.10), checkmate, stats,
SpatialExperiment, methods, SummarizedExperiment, Matrix,
S4Vectors, ggplot2, ggrepel, scales, gridExtra
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
rjson, grDevices, magick, utils, S4Vectors,
SummarizedExperiment, DropletUtils, BiocGenerics, BiocFileCache
BiocGenerics, BiocParallel, methods, rjson, S4Vectors, sf,
SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7),
SummarizedExperiment, stats, utils
BiocParallel, BiocFileCache, data.table, dplyr, edgeR, WGCNA,
flashClust, htmlwidgets, genefilter, ggplot2, ggdendro,
grImport, grid, gridExtra, gplots, igraph, limma, methods,
Matrix, rsvg, shiny, dynamicTreeCut, grDevices, graphics,
ggplotify, parallel, plotly, rappdirs, reshape2, scater,
scuttle, scran, stats, SummarizedExperiment,
SingleCellExperiment, shinydashboard, S4Vectors, tibble, utils,
visNetwork, UpSetR, xml2, yaml
BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicInteractions, GenomicRanges, ggplot2, IRanges,
matrixStats, motifmatchr, S4Vectors, stats,
SummarizedExperiment, TFBSTools, utils
methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices,
stats, tools, utils, fs, BiocGenerics
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges, utils
apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3),
gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3),
plotly (>= 4.9.0), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan
(>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices,
stats, utils, vroom, ComplexHeatmap, dittoSeq, spatstat.geom,
alphahull, methods, spatstat.explore, raster, sp, elsa, Rtsne,
umap, rlang, graphics, SummarizedExperiment
ggplot2, concaveman, BiocParallel, spatstat.explore,
spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4,
methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats,
data.table, dplyr, tidyr, scam, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, ggforce
httr, igraph, utils, stats, miRNAtap, miRNAtap.db,
AnnotationDbi, org.Hs.eg.db, gdata
stats, scales, bamlss, methods, tools, IRanges, Biostrings,
GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome,
S4Vectors, graphics, ggplot2, utils
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
BiocGenerics, BiocParallel, checkmate (>= 2.0.0), edgeR,
fitdistrplus, ggplot2, locfit, matrixStats, methods, scales,
scater (>= 1.15.16), stats, SummarizedExperiment, utils,
crayon, S4Vectors, grDevices
ompBAM, methods, stats, utils, tools, parallel, magrittr, Rcpp
(>= 1.0.5), data.table, fst, ggplot2, AnnotationHub,
BiocFileCache, BiocGenerics, BiocParallel, Biostrings,
BSgenome, DelayedArray, DelayedMatrixStats, genefilter,
GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, progress,
plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment,
S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard,
rhandsontable, DT, grDevices, heatmaply, pheatmap, matrixStats,
RColorBrewer, XML
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb,
GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools,
GenomicAlignments, graph, Rgraphviz
graphics, ggplot2, seqLogo, Biostrings, biomaRt,
GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz,
IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods,
BSgenome.Mmusculus.UCSC.mm9, googleVis
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse,
caret, dplyr, biomaRt, randomForest, ggridges, cvms,
miRBaseConverter, ComplexHeatmap, ggplot2, MetBrewer, rlang,
tnet, ggpubr, stringr, tidyr
stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment,
SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap,
rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment,
stats
stats, methods, SingleCellExperiment, fitdistrplus, graphics,
edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
DBI, lazyeval, methods, tools, stats, BiocGenerics, RSQLite,
tibble
graphics, grDevices, methods, RColorBrewer, stats, utils
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics
Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb,
rtracklayer, SummarizedExperiment, IRanges, GenomicRanges,
DESeq2, edgeR, baySeq, Rsamtools, GenomicFeatures,
GenomicAlignments, grDevices, Gviz, BiocParallel, BiocStyle,
BiocManager
dplyr, magrittr, rlang, stats, purrr, BiocParallel, graphite,
Rcpp, tibble, ggplot2, ggraph, igraph, reshape2, org.Hs.eg.db,
SummarizedExperiment, edgeR, methods, ggforce, ggnewscale,
pheatmap, utils
GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb,
Gviz, Rsolnp
dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment,
SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2,
tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics,
grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
SpidermiR, graphite, AnnotationDbi, e1071, ROCR, MLmetrics,
grDevices, igraph, reshape2, ggplot2
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
BiocParallel, spatstat.geom, concaveman, tidyverse,
data.table, spatstat.explore, dplyr, tidyr,
SingleCellExperiment, tibble, stringr, tidyselect, ggplot2,
methods, stats
topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2,
scatterpie, viridis, slam, stats, clue, liger, reshape2,
graphics, grDevices, utils
graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2,
pheatmap, grDevices, Seurat, SpatialExperiment,
SummarizedExperiment
dplyr, magrittr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, IRanges, Rsamtools, S4Vectors, grid,
BiocGenerics, ggplot2, reshape2, stats, gridExtra,
TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer,
gplots, hash, plotrix
methods,ontologyIndex, datasets, graphics, stats, utils,
knitr, SummarizedExperiment, S4Vectors, rols
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
ggplot2, ggthemes, grid, gridExtra, methods, scales, sp,
stats, utils
assertthat, Biostrings, stringr, dplyr, methods, rlang,
GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment,
GenomeInfoDb,
Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra,
networkD3, ggrepel, graphics, stats, org.Hs.eg.db,
AnnotationDbi
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
stats, utils, graphics, ggplot2, BiocParallel
utils, stats, tools, Matrix, BiocGenerics (>= 0.37.0),
S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>=
1.13.1), DelayedArray (>= 0.15.10)
assertthat, caret, dplyr, tidyr, rsample, methods, rlang,
utils, Biostrings, stats, SummarizedExperiment
ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr,
dplyr, stringr, purrr, magrittr, igraph, methods
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb,
S4Vectors, GenomicFeatures
VariantAnnotation, assertthat, Biostrings, stringr, dplyr,
methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils
data.table, reshape2, ggplot2, stats, grDevices, graphics,
utils, biomaRt, methods
SummarizedExperiment, dplyr, ggplot2, methods, stats
RColorBrewer, lattice, qvalue, multtest, utils, tools,
Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2),
rmarkdown (>= 1.0)
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices
doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2
seqinr, methods, Biostrings, stringr, BiocGenerics
Rcpp (>= 1.0.8), GenomicRanges, rlang, Biostrings,
rtracklayer, utils, methods, igraph, stats, grDevices,
RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph,
networkD3
GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr,
magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools,
glue, magrittr, methods, plotly, rlang, rstudioapi, shinyAce,
shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus
(>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats,
styler, tibble, utils, vroom (>= 1.3.1), yaml, R6, RSQLite,
openssl
DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr,
ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble,
magrittr, DT, stats
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
ape (>= 5.0), phangorn (>= 2.5), utils, methods
methods, GenomicAlignments, GenomicRanges, IRanges,
BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome,
GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics,
reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot,
graphics, GenomicAlignments, Hmisc
ASSIGN (>= 1.23.1), BiocGenerics, BiocParallel,
ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA,
magrittr, methods, RColorBrewer, reshape2, rlang, ROCit,
S4Vectors, singscore, stats, SummarizedExperiment
downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,
tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite
(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),
IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,
SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>=
1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
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)
AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures,
GenomicRanges, GenomicDataCommons, IRanges, methods,
MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest,
S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
apeglm, biomaRt, DESeq2, Rcpp (>= 1.0.7), SCBN,
SummarizedExperiment, stats, utils
BiocBaseUtils, BiocGenerics, BiocIO, GenomeInfoDb,
GenomicRanges, Matrix, MatrixGenerics, methods, RCurl, readr,
R.utils, S4Vectors, utils
methods, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils
utils, igraph, methods, graphics, stats, BiocParallel
BiocFileCache, dplyr, GenomicRanges, methods,
RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils,
utils
arules, fields, GenomicRanges, graphics, stringr, methods,
stats, gplots
GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices,
dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges, methods, ORFik
methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase,
rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi,
org.Hs.eg.db, utils
tibble, readr, dplyr, magrittr, tidyr, stringi, stringr,
rlang, purrr, tidyselect, preprocessCore, stats, parallel,
utils, lifecycle, scales, SummarizedExperiment, GenomicRanges,
methods, S4Vectors, crayon
SummarizedExperiment, dplyr, tibble, tidyr, ggplot2, plotly,
magrittr, rlang, purrr, lifecycle, methods, utils, S4Vectors,
tidyselect, ellipsis, pillar, stringr, cli, fansi
tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, plotly, utils, S4Vectors,
tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr,
ggrepel, propr, lmtest, plyr
biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools
(>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics,
grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2,
rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>=
1.4.0)
scales, stats, utils, ggplot2, data.table, purrr, dplyr,
VariantAnnotation, GenomicRanges, MatrixGenerics,
bestNormalize, depmixS4, naniar, stringr
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma,
GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid,
stats, methods
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
stats, methods, SummarizedExperiment, corpcor, doParallel,
parallel, ggplot2, tidyr, GGally
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
grDevices, graphics, animation, tibble, dplyr, stringr, purrr,
methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
methods, utils, stats, assertthat, ggplot2
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.27.5)
SummarizedExperiment, BiocGenerics, S4Vectors, Biobase,
BiocParallel, ggplot2, tibble, dplyr, caTools, downloader,
magrittr, methods, reshape2, tidyr, data.table, assertthat,
scales, graphics, grDevices, parallel, stats, utils, limma,
jsonlite
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, splines,
stats, stringr, tibble, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS, BiocParallel, limma
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz,
Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools,
IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix,
Rgraphviz, InteractionSet, graph, utils, rhdf5
mgcv, edgeR, SingleCellExperiment, SummarizedExperiment,
slingshot, magrittr, RColorBrewer, BiocParallel, Biobase,
pbapply, igraph, ggplot2, princurve, methods, S4Vectors,
tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS
methods, stats, Matrix, igraph, S4Vectors,
SummarizedExperiment
biomaRt, data.table, doSNOW, foreach, ggplot2, graphics,
grDevices, igraph, limma, parallel, progress, RedeR, snow,
stats, tidyr, topGO
BiocGenerics, caret, chipseq, e1071, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2,
Rsamtools, rtracklayer, S4Vectors, stats, utils
glmGamPoi, DelayedArray, Matrix, MatrixGenerics,
SummarizedExperiment, HDF5Array, methods, utils, Rcpp
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
ggseqlogo (>= 0.1), grDevices, gridExtra (>= 2.3), methods,
parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats,
TFMPvalue (>= 0.0.8), utils
BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots
hash, ggplot2, stats, methods, igraph, utils, glmnet, vbsr,
grDevices, gplots, gtools, pvclust, R.utils, dqrng,
SummarizedExperiment, BiocParallel, matrixStats
ggplot2, viridis, mgcv, SingleCellExperiment, slingshot,
princurve, Biobase, methods, RColorBrewer,
SummarizedExperiment, grDevices, graphics, rgl
ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,
tidytree (>= 0.3.9), utils
stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2,
hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt,
edgeR, lme4, multcomp
methods, BiocGenerics, utils, ape, rlang, dplyr,
SummarizedExperiment, BiocParallel, IRanges, treeio
RSQLite, RMySQL, lassopv, randomForest, xgboost, 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, WGCNA
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
utils, rtracklayer, Matrix, matrixStats, stats, methods,
graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools,
AnnotationDbi
methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater,
GenomicRanges, IRanges, S4Vectors, scattermore, dplyr,
RColorBrewer, grDevices, stats, SummarizedExperiment, utils
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.6.1)
shinyjs, shinyFiles, plyr, data.table, DT, stringr,
stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr,
pryr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices,
graphics, stats, utils
stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector,
Biostrings, Modstrings, ggplot2, scales
Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods,
httr, IRanges, utils
methods, stringr, BiocGenerics, Biostrings, Structstrings,
S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer,
BSgenome, Rsamtools
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, igraph, grid, gridExtra,
xtable, gtable, scales, R.matlab, grDevices, graphics, stats,
utils, methods
ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv,
mclust, gplots, methods, stats, Matrix, SummarizedExperiment,
DelayedArray, S4Vectors
gridExtra, methods, dtw, class, kmlShape, graphics, cluster,
RColorBrewer, grDevices, knitr, rmarkdown, prettydoc, grid,
ggplot2, latex2exp, stats, SummarizedExperiment, GenomicRanges,
IRanges, S4Vectors
tm, text2vec, tokenizers, textstem, stopwords, data.table,
purrr, DiagrammeR, stats
AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges,
GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2,
Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment,
VariantAnnotation (>= 1.19.9)
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
AnnotationDbi, GenomicFeatures, IRanges, GenomicRanges,
BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel,
stats, methods, utils
SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges,
GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb,
BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb,
tools, utils, methods, Matrix
methods, data.table(>= 1.13.6), Matrix, BiocParallel,
BiocNeighbors, SingleCellExperiment, SummarizedExperiment
AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings,
BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures,
GenomeInfoDb, GenomeInfoDbData, GenomicAlignments,
GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments,
Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny,
shinydashboard, shinyFiles, shinyjs, yaml
magick, cowplot, scales, GenomicRanges, ShortRead, zoo,
ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr,
dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools,
stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments,
RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate,
TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures,
BiocFileCache, rappdirs, fda, BiocGenerics
markdown, shiny, shinyjs, shinyBS,
shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx,
condformat, stringr, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs,
TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx,
Rsamtools, GenomicRanges
AnnotationDbi, BiocFileCache, BiocBaseUtils, rjsoncons,
jsonlite, httr, httpcache, progress
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation, data.table
methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
SingleCellExperiment, SummarizedExperiment, tensorflow,
scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats
MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), 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
methods, stats, IRanges, shiny, shinycssloaders, shinyFiles,
ggplot2
MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0),
iterators, foreach, doParallel, gplots, RhpcBLASctl, progress,
reshape2, remaCor (>= 0.0.11), aod, scales, Rdpack, rlang, lme4
(>= 1.1-10), grDevices, graphics, Biobase, methods, utils,
stats
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges
(>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2),
AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome
(>= 1.47.3), GenomicFeatures (>= 1.31.3)
GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools,
utils, stats, methods, gdsfmt, SNPRelate, SeqArray,
SeqVarTools, DelayedArray, Biostrings, IRanges
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
Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel,
GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7),
BiocParallel, GenomeInfoDb, BSgenome, Biobase
IRanges, GenomicRanges, S4Vectors, parallel, matrixStats,
GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats,
graphics, methods
tools, GenomicRanges, VariantAnnotation (>= 1.29.3),
GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools
basilisk, BiocParallel, cowplot, ggplot2, gridExtra, IRanges,
Matrix, methods, RColorBrewer, reticulate, S4Vectors,
SingleCellExperiment, stats, SummarizedExperiment, utils
methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors,
DelayedArray, basilisk, zellkonverter, scuttle,
SingleCellExperiment, BiocParallel, BiocSingular
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
utils, grDevices, stats, methods, dplyr, purrr, tibble,
magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger
Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr,
RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment,
tidyr, utils
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, AnnotationForge, biomaRt,
dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim,
ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph,
methods, plotly, processx, topGO, RColorBrewer, R.utils,
scales, stats, UpSetR, utils
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
BiocParallel, bluster, ggnewscale, ggplot2 (>= 3.4.0), Matrix,
methods, patchwork, rlang, S4Vectors, scales, scico, sf,
SingleCellExperiment, SpatialExperiment,
SpatialFeatureExperiment, spdep, stats, SummarizedExperiment
cowplot, magrittr, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, graphics
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq2, Biobase
Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache,
BiocParallel, SingleCellExperiment, parallel, methods, stats
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
multtest, qvalue, stats, utils, BiocManager
methods, utils, stats, grDevices, assertthat, S4Vectors,
DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics,
limma, topconfects, dplyr, purrr, ggplot2, rlang, scales,
reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
utils, methods, cli, Biobase, SummarizedExperiment, config,
golem, shiny, DT, ggplot2, dplyr, rlang, stringr,
shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer,
logging
dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>=
2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr
limma, matrixStats, locfit, stats, graphics
mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics
(>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet
(>= 1.5.2), S4Vectors, robustbase, IRanges,
SummarizedExperiment, MsCoreUtils, MsFeatures
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
utils, Biostrings, BSgenome, data.table, GenomicRanges,
IRanges, methods, Rcpp, stringi, S4Vectors, future.apply,
stringr, formattable, stats
methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,
IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb,
reshape2, gridExtra, corrplot, dendextend, GetoptLong,
circlize, gtrellis, doParallel, PMCMRplus, ggbeeswarm,
ComplexHeatmap, KEGGREST, grDevices, Biostrings,
BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils
biomaRt, downloader, edgeR, gplots, graphics, limma,
matrixStats, preprocessCore, readr, RColorBrewer, stats,
quantro
Matrix, basilisk, reticulate, SingleCellExperiment (>=
1.11.6), SummarizedExperiment, DelayedArray, methods,
S4Vectors, utils, cli
variancePartition (>= 1.26.0), limma, EnrichmentBrowser (>=
2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast,
ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
cpp11, BH(>= 1.65.0.1), cytolib, RProtoBufLib
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 1.99.3), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat
S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 1.99.3)
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl,
rmarkdown
BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics,
DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext,
RColorBrewer, pheatmap, viridis
knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0),
gplots, tidyr
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
knitr, testthat, markdown, alpineData, rtracklayer,
ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>=
1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>=
4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat
(>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4)
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
knitr, rmarkdown, testthat, DT, caret, microbiome, tidyverse
knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, usethis
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit,
hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,
AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db,
markdown, BiocStyle, knitr, BiocManager, BiocFileCache
IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR,
Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt,
rmarkdown, HubPub
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData,
rmarkdown, HubPub
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
parallel, knitr, rmarkdown, testthat, withr, readr,
BiocStyle, devtools
knitr, BiocStyle, BiocManager, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi,
TBX20BamSubset, testthat, pasillaBamSubset
DESeq2, airway, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran,
testthat
MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR,
knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, ASICSdata
testthat, BiocStyle, lintr, knitr, rmarkdown
ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi,
BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat
(>= 3.0.0)
BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
MotifDb, trackViewer, testthat, rmarkdown
BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC,
rmarkdown, BiocStyle
covr, BiocStyle, knitr, rmarkdown, RUnit
Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh,
Rtsne, testthat, zoo
affy, AnnotationDbi, BiocManager, diagram, GenomicRanges,
GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS,
mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl,
remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr,
statmod, testthat
airway, ggplot2, testthat, EDASeq, knitr, BiocStyle,
RefManageR, sessioninfo, rmarkdown
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2,
ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3),
DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
coda (>= 0.19-4), testthat, interp, fields, pheatmap,
viridis, rmarkdown, spelling
knitr, rmarkdown, methods, testthat, BiocStyle
BiocStyle, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, magick
knitr, rmarkdown, BiocStyle, testthat, callr
reticulate, knitr, rmarkdown, BiocStyle, testthat
testthat, BiocStyle, knitr, rmarkdown, scran, scater,
bluster, scRNAseq
testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr,
viridis, patchwork, RColorBrewer, Seurat
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
aCGH, affy, limma, snapCGH, beadarray, DNAcopy
testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr,
rmarkdown, dplyr, ggplot2, spelling
knitr, rmarkdown, kableExtra, BiocStyle, SPsimSeq, testthat
knitr, testthat, rmarkdown, AnnotationHub, httr
knitr, BiocStyle, testthat, rmarkdown, markdown
BiocGenerics, RUnit, BiocStyle, minfiData, parallel,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments,
ComplexHeatmap, forcats, scales
BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
rmarkdown, SummarizedExperiment
BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0)
RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown,
downloader, devtools (>= 1.4.1), usethis, BiocStyle, callr
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0)
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,
Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,
flowClust, MSnbase, annotate, RUnit
testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy,
RcppHNSW
knitr, dbplyr, 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, rmarkdown, rhdf5client
airway, BiocStyle, boot, DESeq2, GOSemSim, Hmisc, knitr (>=
1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling,
targetscan.Hs.eg.db, testthat, WGCNA
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, lubridate,
visNetwork, clipr, blastula, kableExtra, DiagrammeR,
SummarizedExperiment
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, xml2, git2r
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr
roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr,
rmarkdown, covr, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, igraph, magick, lgr
BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0),
knitr, rmarkdown, covr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr, covr
BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr
cluster, parallel, GenomicFeatures, dynamicTreeCut,
Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr,
devtools, pander, plotly, randomcoloR
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2,
covr
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db,
ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db,
knitr, omicade4, rmarkdown, testthat
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
knitr, markdown, base, rmarkdown, ggplot2
testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger,
SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1)
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth,
pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10,
BiocStyle
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
RUnit, devtools, BiocGenerics, knitr, rmarkdown
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster
rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0),
utils, testthat
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr,
tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 2.1.0), covr
BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr,
plotly, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, devtools
BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes,
ggplot2, reshape2, Biostrings
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,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat
(>= 1.5.2), BatchJobs
BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>=
3.0.0)
testthat, RUnit, doParallel, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat, BiocStyle, TENxBUSData,
TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38,
EnsDb.Hsapiens.v86
knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm9.knownGene
testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle,
rmarkdown, covr, sessioninfo
BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE,
BiocStyle, knitr, rmarkdown
testthat (>= 3.1), knitr, rmarkdown, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl,
gplots
BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat,
VGAM
RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0),
sessioninfo
BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
rmarkdown, testthat, uwot
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma,
lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter, rmarkdown
phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia,
purrr
BiocStyle, knitr, survival, survminer, rmarkdown, testthat
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
SingleCellExperiment, mclust, testthat (>= 3.0.0)
crossmeta, knitr, rmarkdown, testthat, lydata
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
BiocManager, BiocStyle, TENxPBMCData, singleCellTK,
M3DExampleData
testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle,
ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment,
scater, broom.mixed, cowplot, igraph, ggraph
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr,
destiny, ggrepel
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics,
BiocManager, kableExtra, rgl
BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics,
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db,
Biobase, tools
zellkonverter, SingleCellExperiment, HDF5Array, BiocStyle,
knitr, rmarkdown, testthat (>= 3.0.0), mockery
BiocStyle, knitr, rmarkdown, testthat, ggplot2
knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater,
scMerge, fgsea, escape, pheatmap, patchwork
airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools
(>= 2.3.0), BiocStyle, testthat
ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager,
rmarkdown
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager,bibtex
knitr, rmarkdown, Matrix, testthat, vdiffr
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
Rsamtools, GenomicInteractions, GenomicRanges, IRanges,
AnnotationHub
testthat, roxygen2, devtools, knitr, lintr
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle,
gridExtra (>= 2.2), testthat
AnnotationHub, BSgenome, limma, reactome.db, BiocManager,
BiocStyle, BSgenome.Ecoli.NCBI.20080805,
BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
knitr, rmarkdown, testthat, trackViewer, motifStack,
OrganismDbi
clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram,
ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
testthat, knitr, markdown, rmarkdown, BiocStyle, Signac,
future, igraph, bluster, httr
BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3),
GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3),
testthat
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown,
rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
BiocStyle, knitr, rmarkdown, testthat, webshot
knitr, testthat, ReactomePA, RUnit, BiocGenerics,
AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db,
biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods,
Biostrings,Homo.sapiens, R.utils
testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra,
ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BiocManager,
knitr, rmarkdown, testthat, R.utils, BiocStyle
knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle,
pkgdown
limma, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>=
2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE,
knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges,
robustbase, glmnet, class, randomForestSRC, MatrixModels,
xgboost
BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.36.5)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
knitr, rmarkdown, bookdown, testthat, BiocStyle
knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr,
CluMSIDdata, metaMS, metaMSdata, xcms
BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph,
rmarkdown
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc,
ReactomePA, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2,
purrr
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
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
minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph
VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR,
rmarkdown, devtools, cowplot, usethis, scales, testthat,
GenomicRanges, cn.mops, R.utils
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment,
TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR,
rmarkdown
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
rmarkdown, covr
BiocStyle, knitr, markdown, testthat (>= 3.0.0)
genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
flexclust, randomForest, e1071
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
BiocStyle, knitr, RUnit, BiocGenerics, showtext
BiocStyle, corrplot, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
covr, testthat, knitr, Rcpp, rmarkdown, markdown
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0),
genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown,
phytools, phangorn, testthat, ggtree, tidytree, statmod, covr
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo
knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
MsBackendMgf
knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats,
dynamicTreeCut, testthat
knitr, testthat, rmarkdown, covr, viridis, ggplot2,
RColorBrewer, randomForest, tidyr, TSCAN
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
BiocStyle, knitr, rmarkdown, minfiData, RCurl
BiocStyle, knitr, rmarkdown, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
RColorBrewer, gplots, BiocStyle, knitr, rmarkdown
pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
testthat
ade4, BiocStyle, CellBench, DuoClustering2018, knitr,
rmarkdown, scater, testthat
Biobase, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, piano, ggplot2
testthat (>= 3.0.0), spelling, knitr, data.table, R.utils,
tidyverse, rmarkdown, htmlwidgets, MASS, factoextra, Rtsne,
plotly, dendextend, BiocStyle, cowplot
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
testthat
biomaRt, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7),
knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice,
MASS, tensorflow, testthat
BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown,
rtracklayer, sangerseqR, testthat, VariantAnnotation
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr,
rmarkdown, rtracklayer, testthat, utils
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
AnnotationDbi, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr,
igraph, dplyr
testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat,
shinytest
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
XML, grImport, grImport2, BiocStyle, knitr, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph,
diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR,
factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster,
forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr,
norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr,
limma, preprocessCore, stringr, tidyr, impute, gplots,
grDevices, reshape2, graphics, stats, methods, ggplot2,
RColorBrewer, Matrix, org.Sc.sgd.db
AnnotationFilter, BiocStyle, covr, ensembldb, GenomicState,
knitr, lifecycle, markdown, recount, RefManageR, rmarkdown,
sessioninfo, testthat, tibble
EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa,
SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle,
edgeR
knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR,
cowplot, ggplotify, dagitty, lmtest, sandwich, devtools,
curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel,
docopt, CARNIVAL
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens,
rmarkdown
testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>=
1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2),
reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools
(>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator,
RefManageR
glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell,
SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr,
pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo,
pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel,
patchwork
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, rmarkdown, SeqArray, GDSArray
testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark,
profmem, HDF5Array
testthat, knitr, BiocStyle, rmarkdown, Matrix
markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr,
dplyr, reticulate
BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat
uwot, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble,
ggplot2, missForest, pheatmap, RColorBrewer, ggrepel,
ggbeeswarm
BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>=
0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma,
RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, covr
sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19),
RefManageR, rmarkdown (>= 0.3.3), testthat, covr
biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData
(>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>=
2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3),
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr
BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq,
RUVSeq, RColorBrewer, statmod
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer,
apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,
airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager
knitr, rmarkdown, igraph, testthat, FNN, tidyverse,
gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,
org.Mm.eg.db, scran, repr
knitr, rmarkdown, testthat, BiocStyle, IHW
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr, rmarkdown, testthat
knitr, akima, lattice, scales, gridExtra, latticeExtra,
rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2, utils
testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools,
ggplot2, gridExtra, ggpubr, grid, magick, hexbin
lattice, parallel, MASS, RColorBrewer, xtable
plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR,
ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq,
ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran
knitr, RUnit, BiocGenerics,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata
knitr, rmarkdown, testthat, sessioninfo, BiocStyle,
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
prettydoc, clusterProfiler, gson (>= 0.0.5), knitr,
rmarkdown, org.Hs.eg.db, testthat
covr, testthat, knitr, rmarkdown, BiocStyle
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
testthat, knitr, BiocStyle, rmarkdown, jsonlite,
DropletTestFiles
RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT,
EnsDb.Hsapiens.v86
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
limma, convert, GEOquery, dyebiasexamples, methods
knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager,
devtools
distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq,
statmod
BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr,
rmarkdown, RUnit (>= 0.4.32)
BiocStyle, digest, knitr, rmarkdown, shiny
ecoliLeucine, ecolicdf, graph, multtest, affy
BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR,
KernSmooth, testthat, DESeq2, rmarkdown
jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi,
SummarizedExperiment, org.Hs.eg.db
knitr, tximportData, testthat (>= 3.0.0)
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38,
ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer
BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat,
data.table, DT, GenomicInteractions, webshot, R.utils, covr,
sesameData
ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla,
airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown
knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb,
testthat, TFBSTools
minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown
clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown,
org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi,
ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0),
ggstar, treeio, scales, tidytree, ggtreeExtra, tidydr
BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
1.20.0), magrittr, rmarkdown, AnnotationHub
RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
badger, BiocFileCache, BiocParallel, parallel, BiocStyle,
clusterProfiler, GenomicAlignments, grDevices, htmlwidgets,
knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
UpSetR, plyranges, scales, Matrix, consensusSeekeR
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
testthat, knitr, rmarkdown, BiocStyle,
BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData
knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
BiocStyle, clusterProfiler, karyoploteR, knitr, org.Hs.eg.db,
regioneR, Seurat, survival, survminer,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics
testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra,
methods, grDevices
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown,
EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
Matrix, BiocStyle, knitr, rmarkdown, magrittr, kableExtra,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, httptest,
AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3,
TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, roxygen2, knitr, Biobase, SummarizedExperiment,
antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle,
minfi, rmarkdown
testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors,
IRanges, SummarizedExperiment, antiProfilesData,
hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny,
minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr,
AnnotationHub
testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus,
TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown,
BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer,
utils, RMySQL, DBI, matrixStats
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat,
webshot
Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle,
testthat, dittoSeq (>= 1.1.2)
ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
readxl, memoise, markdown, sctransform, DESeq2, MAST,
DelayedMatrixStats, cowplot, ggdendro, grDevices, grid,
gridExtra, scales, magick, badger
GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub
BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran,
scater, scds, TENxPBMCData, airway
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
BiocStyle, covr, knitr, plyranges, rmarkdown, testthat (>=
3.0.0), tidyverse
AnnotationHub (>= 2.22), BSgenome (>= 1.58),
BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown,
markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>=
1.5), tidyverse (>= 1.3), covr, patchwork
BiocStyle, knitr, rmarkdown, testthat, BiocManager
BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown,
spelling, testthat (>= 3.0.0)
caret, mlbench, SingleCellExperiment, knitr, rmarkdown,
testthat, BiocManager
testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData,
scater, schex, gridExtra, scran, Seurat, knitr, rmarkdown
rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0),
BiocStyle
biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit
RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics,
org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation
BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>=
3.0.0), TxDb.Athaliana.BioMart.plantsmart28
testthat, knitr, rmarkdown, macrophage, tximeta,
org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma,
ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi,
pheatmap, Gviz, GenomeInfoDb, data.table
BiocStyle, GEOquery, knitr, rmarkdown, markdown,
BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto, flowStats(>= 4.7.1)
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
RUnit, BiocGenerics, knitr, markdown, rmarkdown
BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0)
BiocStyle, testthat, CytoML, flowWorkspace, ggrepel,
scattermore, pheatmap, ggpointdensity
testthat, knitr, rmarkdown, BiocStyle, DepecheR
xtable, testthat, openCyto, ggcyto, ggridges
knitr, rmarkdown, ggplot2, BiocGenerics, stats, flowClust
colorspace, flowStats, knitr, rmarkdown, markdown, testthat
testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown,
ggcyto, parallel, CytoML, openCyto
BiocStyle, covr, ggrepel, kableExtra, knitr,
metabolomicsWorkbenchR, POMA, rmarkdown, rvest,
SummarizedExperiment, testthat (>= 2.3.2), tidyverse
BiocStyle, knitr, rmarkdown, testthat, covr,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene
pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase,
Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db,
BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2,
ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap,
viridis
RUnit, rentrez, knitr, rmarkdown, BiocStyle
assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat
apcluster, GEOquery, knitr, rmarkdown, BiocStyle
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret,
survival, BiocStyle, magick, rmarkdown
RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny,
STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data, geneplast.data.string.v91,
ggplot2, ggpubr, plyr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
CompQuadForm, COMPoissonReg, poibin, SPAtest, survey,
testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr,
ggplot2, GGally, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, BiocStyle, htmltools, clusterProfiler, macrophage,
org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
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
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods
BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown,
RUnit
spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr
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
BiocStyle, knitr, rmarkdown, DT, testthat, listviewer,
ggplot2, GenomicAlignments, Rsamtools, BiocParallel,
TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools,
R.utils, data.table
AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle,
rmarkdown, GenomicDistributionsData
RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome,
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3
(>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Celegans.UCSC.ce11.ensGene,
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,
AnnotationFilter, RUnit, BiocStyle, knitr, markdown
BiocStyle, RUnit, genefilter, deepSNV, snpStats,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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, KEGGREST, 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,
rmarkdown, BiocStyle
RUnit, 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,
shiny, shinyjs, shinycustomloader, data.table, DT, magrittr,
shinydashboard
knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
BiocStyle, testthat, forcats, stats, wordcloud, circlize,
EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
utils
testthat, knitr, BiocStyle, rmarkdown, covr
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
rmarkdown, knitr, usethis, testthat (>= 3.0.0)
BiocCheck, roxygen2, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph,
Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat,
EnsDb.Hsapiens.v75, tinytex
testthat, flowWorkspaceData, knitr, rmarkdown, flowStats,
openCyto, flowViz, ggridges, vdiffr
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown,
GenomicRanges
ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown,
readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix,
scater, scran, uwot, testthat (>= 3.0.0)
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue
aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust,
rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, IRanges,
GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat,
MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran, Matrix
testthat, knitr, rmarkdown, survival, survcomp, pROC,
VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle,
BiocManager
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics
knitr, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6,
BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene,
TxDb.Rnorvegicus.UCSC.rn7.refGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, IHW, clusterProfiler,
ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>=
3.0.0), BiocStyle, csaw, BiocParallel, robust,
variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools,
motifmatchr, rbioapi
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
checkmate, 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)
BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr
BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat
SummarizedExperiment, knitr, plotly, WGCNA, rmarkdown
knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp,
Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP,
iC10TrainingData, pamr, testthat
BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma,
RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny,
shinydashboard, ggplot2, data.table, plotly, future, promises,
shinybusy, shinyjs
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Hs.eg.db, testthat (>= 3.0.0)
BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr,
rmarkdown, testthat
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, qqman
DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz,
Rsamtools, rtracklayer, graph, ggbio, DelayedArray,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
VariantAnnotation, parallel
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
LoomExperiment, SummarizedExperiment, SingleCellExperiment,
S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown,
BiocStyle
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter,
GenomicFeatures, RUnit, SingleCellExperiment
BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown,
statmod, testthat (>= 2.0), vdiffr, withr
BiocStyle, testthat, knitr, rmarkdown, seqCNA
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
knitr, doParallel, testthat, BiocGenerics, markdown
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix,
BiocFileCache, rappdirs
knitr, rmarkdown, testthat, BiocStyle, BiocManager
cowplot, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
knitr, annotate, gwascat, testthat, rmarkdown
knitr, rmarkdown, markdown, devtools, BiocStyle
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat, rmarkdown
knitr, BiocManager, qpdf, hpar, testthat, rmarkdown
rmarkdown, colorspace, e1071, kernlab, ranger,
SummarizedExperiment, Biostrings, randomForest, gprofiler2,
gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools,
knitr
EDASeq, testthat, knitr, rmarkdown, BiocStyle
AnnotationHubData, ExperimentHubData, testthat, knitr,
rmarkdown, BiocStyle,
knitr, BiocStyle, beeswarm, tximportData, DT, tximport,
dplyr, magrittr, BiocFileCache, testthat, rhdf5client,
rmarkdown
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, Rsubread (>= 1.29.0), testthat
testthat, BiocStyle, airway, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
knitr, rmarkdown, msa, ape, testthat, seqinr
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, gridExtra, ggrepel
RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown,
testthat
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
BiocGenerics,BiocManager, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19,
EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown,
rmarkdown, rtracklayer, RUnit, grDevices,
TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene
knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges,
data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap,
cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3,
GOexpress, SingleCellExperiment, scater, gplots, pheatmap,
airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve
(>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks
RUnit, hgu95av2.db, knitr, GenomicRanges,
SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer,
metagenomeSeq, gplots, vegan, Biobase
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
roxygen2, vegan, withr, extraDistr, ggalluvial, scales,
gridExtra, R.utils, RefManageR, flexdashboard, circlize,
plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap,
BiocParallel, progressr, future, doFuture, foreach, psych,
data.table, Rcapture
testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq,
TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer,
viridis, htmltools
BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0), scRNAseq, scater
BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0), nullrangesData
scRNAseq, scater, scran, airway, edgeR, AnnotationDbi,
org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown,
BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr
BiocStyle, knitr, rmarkdown, htmltools, RUnit
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db,
pheatmap, BiocStyle, testthat
knitr, png, limma, grid, DT, randomForest, digest, testthat,
rmarkdown
BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db,
pasillaBamSubset
RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,
SPIA
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats,
VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75,
Rsamtools, GenomicFiles (>= 1.13.6)
knitr, rmarkdown, curatedMetagenomicData, BiocStyle,
testthat, pkgdown, covr, withr
affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db,
gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines,
statmod (>= 1.2.2), vsn
BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer,
moments, testthat
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr,
spelling, testthat
parallel, testthat, knitr, BiocStyle, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, reticulate
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
ROCR, knitr, M3DExampleData, scater, SingleCellExperiment,
monocle, Seurat, Biobase
knitr, rmarkdown, bookdown, testthat, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10
knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown,
markdown
testthat, knitr, rmarkdown, BiocStyle, MACSdata
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors, pheatmap, curl
gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil,
rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools,
BiocGenerics, BiocManager
biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap,
png, scales, sva, BiocManager
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
knitr, rmarkdown, BiocStyle, testthat, covr
biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>=
2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>=
0.12.2), knitr, testthat, readr, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, AnnotationHub
signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench
knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(>
6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer,
BiocStyle, scater, DelayedArray, Matrix, HDF5Array, zinbwave,
dplyr
sparseMatrixStats, DelayedMatrixStats, SummarizedExperiment,
testthat (>= 2.1.0), Matrix
knitr, markdown, BiocStyle, testthat (>= 3.0.0)
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
testthat (>= 3.0.0), knitr, rmarkdown, devtools, impute
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k,
knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
testthat, knitr, rmarkdown, fgsea, BiocManager
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0)
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
cowplot, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0),
knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1),
rmarkdown, covr
shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), org.Hs.eg.db, clusterProfiler,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra,
knitr, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny,
shinyjs, DT, AnnotationHub
BiocStyle, covr, knitr, HDF5Array, rmarkdown, structToolbox,
testthat, pmp, grid, png
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown
BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay, IHW
knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2),
UpSetR
BiocManager, BSgenome, knitr, RMySQL, RUnit
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, ExperimentHub, tidyr, rmarkdown
BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr
(>= 1.11), testthat (>= 2.2.1)
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel,
downloader, R.utils, doParallel, reshape2, JASPAR2022,
TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper,
stageR, BiocFileCache, png, htmltools, knitr, jpeg,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19
knitr, rmarkdown, DSS, bsseq, plotly,
BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38,
MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings,
RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0)
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
RUnit
rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics,
BiocStyle, tidyr, ggplot2
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit,
methInheritSim
testthat (>= 2.1.0), knitr, rmarkdown, genomation,
BiocManager
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0),
covr
lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
parallel, rtracklayer, Biostrings, TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2,
stringr, biomformat, reldist, ade4, microbiomeDataSets,
rmarkdown
knitr, rmarkdown, BiocStyle, testthat, patchwork,
microbiomeDataSets
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
testthat, covr, glmnet, Matrix, kernlab, e1071, ranger,
knitr, rmarkdown, BiocStyle, withr
rmarkdown, prettydoc, testthat, knitr, nlme, phangorn,
DECIPHER, randomForest, jsonlite, biomformat, scales, yaml,
withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset,
ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats,
phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel,
shadowtext, DirichletMultinomial
BiocStyle, breastCancerMAINZ, breastCancerNKI,
breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP,
breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit
testthat, MASS, mvtnorm, scater, scran, covr, knitr,
rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData,
MouseThymusAgeing, magick, RCurl, curl, graphics
knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind,
affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1
biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX, future, future.apply
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
human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, RUnit
scRNAseq, scater, BiocStyle, knitr, rmarkdown
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
BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
BiocStyle, knitr, rmarkdown, R.cache, SPONGE
BiocStyle, edgeR, knitr, minfiData, rmarkdown,
tweeDEseqCountData, DMRcate, ExperimentHub
BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml,
kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0),
xgboost
BiocStyle, knitr, rmarkdown, testthat, rgl
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party, klaR,
testthat
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz,
GOstats, graph, limma, mouse4302.db, reactome.db
testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle,
MMAPPR2data
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM
testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown,
markdown, covr, BiocStyle
testthat, msdata (>= 0.35.3), knitr (>= 1.1.0), roxygen2,
BiocStyle (>= 2.5.19), rmarkdown
testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny,
shinyFiles, shinydashboard, shinyjs
knitr, testthat, Seurat, ggpubr, foreach, psych,
MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
data.table, tidyverse, BiocStyle, Matrix, markdown
BiocStyle, knitr, rmarkdown, testthat, viper
JASPAR2020, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat,
BiocStyle, gridExtra
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
BSgenome.Hsapiens.UCSC.hg19,
SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown,
BSgenome.Drerio.UCSC.danRer7, BiocStyle
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR,
markdown
grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer,
BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020
Biobase, knitr, seqinr, ape (>= 5.1), phangorn
rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, rmarkdown
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown
BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr,
lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5),
testthat
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown, rpx, mzR, msdata
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2,
tinytest
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
BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2)
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata,
MSnbase, matrixStats, MsCoreUtils, covr
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr,
SingleCellMultiModal, CiteFuse, scater
BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>=
2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival,
survminer, testthat
knitr, rmarkdown, gplots, RUnit, BiocGenerics,
preprocessCore, Biobase, GEOquery
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr,
magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene
brgedata, minfi, minfiData, knitr, rmarkdown, testthat,
omicade4, iClusterPlus, GEOquery, MultiAssayExperiment,
BiocStyle, RaggedExperiment
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db,
org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, metaboliteIDmapping,
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
org.Mm.eg.db, rlang, markdown, attempt, processx, testthat,
knitr, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, scater, bluster,
DropletUtils, scRNAseq
SNPlocs.Hsapiens.dbSNP144.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
SNPlocs.Hsapiens.dbSNP155.GRCh37,
SNPlocs.Hsapiens.dbSNP155.GRCh38,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors,
rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR,
BiocStyle, covr, Rsamtools, MatrixGenerics, badger,
BiocParallel, GenomicFiles
BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr,
phylogram, RColorBrewer, reshape2, rmarkdown, statmod,
testthat, UpSetR
testthat, BiocStyle, knitr, rmarkdown, survival, XVector,
qpdf, covr
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), ccfindR
(>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr,
rmarkdown
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat, BiocManager, rmarkdown
DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1),
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown,
rtracklayer, testthat (>= 3.0.0), covr
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
knitr, RUnit, BiocGenerics, BiocStyle, rmarkdown, markdown
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache, SeuratObject
AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db,
rmarkdown, testthat (>= 3.0.0), tidyverse
paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown,
testthat, cgdsr
curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3,
clusterExperiment, netSmooth, scater
mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr,
rmarkdown, knitr
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db,
org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr,
markdown
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp,
BiocStyle, knitr
BiocStyle, Cairo, knitr, testthat, truncnorm
BiocStyle, knitr, rmarkdown, STexampleData, scran, ggplot2,
testthat
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr,
TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene,
testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown,
TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Mm.eg.db,
org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics,
org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2,
BiocStyle
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub,
ExperimentHub, nullrangesData, excluderanges, ensembldb,
EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener,
magrittr, tidyr, cobalt
knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg,
DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
BiocStyle, covr, knitr, recount, RefManageR, rmarkdown,
sessioninfo, SummarizedExperiment, testthat (>= 3.0.0),
GenomicFeatures, xfun
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, ACME, RCurl
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, VanillaICE, crlmm
BiocStyle, knitr, rmarkdown, snpStats, brgedata
knitr, rmarkdown, testthat, devtools, BiocManager
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
knitr, rmarkdown, BiocStyle, magick, testthat
BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph,
gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers,
Rgraphviz, smoof, supraHex, testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
testthat (>= 3.1.4), jsonlite, knitr, rmarkdown
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle,
SingleCellExperiment, celldex, rmarkdown, AnnotationDbi
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
testthat, rmarkdown, knitr, BiocStyle,
BSgenome.Hsapiens.UCSC.hg19
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat,
knitr, rmarkdown, BiocStyle, ggplot2
Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19,
AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer,
biomaRt, RUnit, RMariaDB
rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown,
testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape,
phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
testthat, knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB,
AnnotationDbi, beeswarm, covr
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
biomartr, knitr, rmarkdown, testthat, dendextend, biocViews,
BiocCheck, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA,
ggplot2, ggrepel, car, cowplot
bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools,
GenomicFeatures, annotate
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3,
knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR,
devtools, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea,
ComplexHeatmap, GGally, ggsignif, circlize, enrichplot,
ggnewscale, tidyverse, cowplot, ggfittext
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer,
foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2,
airway, org.Hs.eg.db, magrittr, rmarkdown
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander,
BiocStyle
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr,
knitr, rmarkdown, pkgdown
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown, BiocStyle
BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4,
rmarkdown, testthat
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq,
SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr,
mia
BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr,
withr
testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown,
org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle,
stringr, calibrate
foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr,
rtracklayer, ggbio, Gviz, data.tree, jsonlite
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>=
2.30.0), knitr, AnnotationDbi, energy
ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr,
rmarkdown
AnnotationDbi, AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures,
GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr,
org.Hs.eg.db, rtracklayer, plotgardenerData, png, rmarkdown,
scales, showtext, testthat (>= 3.0.0),
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, htmltools, BiocStyle, rmarkdown, testthat
knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0),
HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19,
pasillaBamSubset, covr, ggplot2
testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
magick
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle
BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse,
testthat (>= 2.3.2)
BiocStyle, knitr, rmarkdown, colr, metap, repmis
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
testthat, rmarkdown, knitr, Rtsne, gridExtra
knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra,
roxygen2, testthat (>= 2.1.0), spelling
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown
BiocStyle, testthat, knitr, rmarkdown, png, Cairo
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl,
pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
BiocStyle, gridExtra, grid, testthat, devtools, knitr,
rmarkdown, ComplexHeatmap
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable,
rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, akima,
fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals,
reshape, magick
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat
(>= 3.0.0)
BiocStyle, BiocManager, testthat, shinyTree, knitr,
colourpicker, gtools, XML, R.utils, RColorBrewer, DT,
shinyWidgets, sass, rclipboard
BiocStyle, knitr, rmarkdown, igraph, ComplexHeatmap, viridis,
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment,
BiocStyle, rmarkdown, knitr, factoextra, testthat
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
pumadata, affydata, snow, limma, ROCR,annotate
BiocParallel, BiocStyle, PSCBS, R.utils,
TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr,
optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat
MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel,
PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background,
BiocStyle, knitr
affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown
SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2,
gplots, dplyr, limma, magrittr, DT, shiny, shinydashboard,
testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore,
matrixStats, imputeLCMD, pcaMethods, impute, norm,
ComplexHeatmap
limma, Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures,
impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle,
knitr, rmarkdown
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
gridExtra, knitr, qPLEXdata, rmarkdown, testthat, UniProt.ws,
vdiffr
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown, BiocManager, MASS
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR,
rmarkdown, sessioninfo, testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr,
rmarkdown, covr, testthat
QUBICdata, qgraph, fields, knitr, rmarkdown
BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene,
biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny,
ChIPpeakAnno
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
rmarkdown, BiocStyle, knitr, pander, markdown
BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
limma, biomaRt, RUnit, BiocGenerics, BiocStyle
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel, rmarkdown
Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
gplots, rtracklayer, igraph, knitr,
RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat,
visNetwork
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
knitr, rmarkdown, testthat, stringr, networkD3, visNetwork,
wesanderson
testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase,
devtools
BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,
prettydoc, testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
knitr, rmarkdown, testthat (>= 2.1.0), here
AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2,
sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>=
1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4),
rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT,
edgeR, ggplot2, RColorBrewer
BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown,
testthat, pryr, interactiveDisplayBase, recount
minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown,
BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager,
BSgenome, RMySQL
BiocStyle, knitr, rmarkdown, markdown, TreeAndLeaf
GEOquery, rmarkdown, knitr, BiocManager, testthat
BiocStyle, knitr, rmarkdown,
BSgenome.Hsapiens.UCSC.hg19.masked, testthat
rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>=
3.0.0)
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2),
ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, minfiDataEPIC
RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla,
org.Sc.sgd.db, rmarkdown, markdown
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db,
BiocStyle, restfulSEData, rmarkdown
mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, ggplot2, tibble, lipidr
RUnit, BiocStyle, BiocGenerics, xtable, sna
testthat (>= 0.3), knitr, rmarkdown, BiocManager,
org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
boot, tools, BiocGenerics, knitr, xtable
bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark,
dplyr, ggplot2, mockery
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), rhdf5 (>=
2.34.0)
BiocStyle, knitr, rmarkdown, tinytest, mockery
testthat, rmarkdown, knitr, BiocStyle, BSgenome,
BSgenome.Hsapiens.UCSC.hg19
knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10,
edgeR, limma, testthat, rmarkdown
rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr,
jsonlite, kableExtra, kernlab, knitr, magick, MASS,
org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart,
testthat (>= 3.0.0), tibble, tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger
BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1),
CAMERA, RUnit, knitr, rmarkdown
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
Biostrings, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data,
RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer,
keras
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
RNAmodR.Data
knitr, rmarkdown, png, grid, RNASeqRData
Category, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19,
RnBeads.mm9, 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,
MethylSeekR, sesame
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat,
lubridate, DT, rmarkdown,
BiocGenerics, BiocStyle, knitr, multtest, omicade4,
rmarkdown, testthat
knitr, rmarkdown, testthat, RUnit, BiocGenerics
BiocStyle, covr, kableExtra, knitr, rmarkdown, styler,
testthat (>= 3.0.0)
Biostrings, BiocStyle, testthat, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0),
shinydashboard, DT, plotly, heatmaply, magrittr, utils,
clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db,
org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db,
org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db,
org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db
GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
Biostrings, methods, knitr, rmarkdown, BiocStyle
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, magrittr, tidyr
BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit,
BiocGenerics
knitr, BiocStyle, TPP, testthat, rmarkdown
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
RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,
Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db,
org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
testthat, BiocStyle, knitr, rmarkdown, BridgeDbR
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
parallel, crayon, RUnit, knitr, markdown, rmarkdown,
BiocGenerics, SNPRelate, ggmanh
BiocGenerics, BioNet, DLBCL, formatR, knitr, msm,
org.Sc.sgd.db, markdown, rmarkdown, RUnit
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Rnorvegicus.UCSC.rn6
Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown,
rhdf5, HDF5Array
BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq,
robustbase, rmarkdown, testthat, Biobase
BiocStyle, knitr, testthat, cluster, SingleCellExperiment
testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle,
rmarkdown
BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat,
tidySingleCellExperiment, loo
PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra,
rmarkdown
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize,
ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown,
RColorBrewer, ReactomePA, clusterProfiler, cowplot,
org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne,
BiocParallel, e1071, WGCNA, devtools, DOSE
ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr,
TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran
knitr, markdown, rmarkdown, scater, scattermore, scales,
matrixStats, deldir
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
scater, testthat, badger
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase,
BiocGenerics, ggplot2, ggthemes
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork,
doParallel, BatchJobs, splatter, scater, kableExtra, mclust,
TENxPBMCData
knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2,
impute, scater, sva, preprocessCore, vsn, uwot
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra,
knitr, locStra, plotly, rmarkdown, RColorBrewer, readr,
reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap
testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq,
dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle,
Biobase, pheatmap, scater
testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater
markdown, BiocGenerics, covr, DuoClustering2018, ggplot2,
knitr, rmarkdown, TENxPBMCData, testthat
testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s,
metagenomeSeq, epivizrStandalone, GenomeInfoDb
BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
testthat, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22),
rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>=
0.3.0)
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
emojifont, knitr, rmarkdown, prettydoc, tibble
testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr,
knitr, rmarkdown, testthat
scales, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown,
testthat, tidyr, BiocStyle, ggrepel, grDevices, pals
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
testthat, parallel, knitr, rmarkdown, BiocStyle
knitr (>= 1.30.0), mCSEA (>= 1.10.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICmanifest, testthat, minfiData
shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse,
ggpubr
org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
knitr, testthat, rmarkdown, BiocStyle, signatureSearchData,
DT
BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR,
limma
IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr,
rmarkdown
curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>=
3.0.0)
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph
BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan,
igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics,
clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust,
BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny,
shinydashboard, cola, hu6800.db, rmarkdown, genefilter,
gridtext, fpc
BiocStyle, knitr, biomaRt, stringr, monocle
testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>=
2.9.1), Rtsne
testthat, Rsubread, BiocStyle, knitr, lintr, spelling,
org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS,
shinyjqui, shinyWidgets, shinyFiles, BiocGenerics,
RColorBrewer, fastmap (>= 1.1.0), harmony
BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr,
parallel, rmarkdown, readr, SingleMoleculeFootprintingData,
testthat (>= 3.0.0)
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scater, scran, scRNAseq,
ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
BSgenome, knitr, rmarkdown, RMySQL, RUnit
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat
(>= 2.1.0)
knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0)
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown,
testthat
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr,
PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown,
SummarizedExperiment, statmod, stringr, testthat, webshot
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5,
BiocStyle, testthat, knitr,
RefManageR, BiocStyle, knitr, testthat (>= 3.0.0),
sessioninfo, rmarkdown, markdown
knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix
BiocStyle, DropletUtils, knitr, Matrix, rmarkdown, SFEData,
testthat (>= 3.0.0)
av, knitr, rmarkdown, BiocStyle, BiocSingular, RUnit,
BiocGenerics, DESeq2, distinct, HDF5Array, kableExtra, magick,
ExpressionAtlas, DT, Biobase, GEOquery, pROC, rols,
shinyWidgets, shinyjs, htmltools, shinyBS, sortable
BiocManager, Biostrings, knitr, pheatmap, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
BiocStyle, knitr, rmarkdown, pkgdown, testthat, xROI
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
covr, testthat, equatiomatic, universalmotif, kebabs,
ComplexHeatmap, rmarkdown, markdown, knitr, devtools,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
BiocStyle, covr, cowplot, magick, knitr, limSolve, lme4,
progress, pscl, testthat, preprocessCore, rmarkdown, scDD,
scran, mfa, phenopath, BASiCS (>= 1.7.10), zinbwave, SparseDC,
BiocManager, spelling, igraph, scuttle, BiocSingular,
VariantAnnotation, Biostrings, GenomeInfoDb, GenomicRanges,
IRanges
knitr, rmarkdown, openssl, crayon, egg, DESeq2, limma,
DoubleExpSeq, satuRn, edgeR, Rsubread, testthat (>= 3.0.0)
testthat, knitr, rmarkdown, ggplot2, tidyr
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI
testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
digest, doParallel, bigmemory
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils,
spelling
BiocStyle, colorBlindness, ExperimentHub, DelayedArray,
ggcorrplot, grid, igraph, jpeg, knitr, methods, png, rmarkdown,
scater, scatterpie, scran, Seurat, SeuratObject,
SpatialExperiment, SummarizedExperiment, S4Vectors,
TabulaMurisSenisData, TENxVisiumData, testthat
BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3),
RUnit
knitr, rmarkdown, LSD, testthat, BiocStyle
RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray
knitr, BiocStyle, rmarkdown, tinytest, doFuture
knitr, rmarkdown, testthat, BiocManager, BiocStyle
BiocManager, BiocStyle, cowplot, DT, htmltools, knitr,
pander, rmarkdown, spelling, stringr, testthat (>= 3.0.0),
tidyverse
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr,
ggrepel, cluster, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
qgraph, png, grid
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots,
gridExtra, hash, dplyr, parallel
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx,
ggplot2, magick
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
agricolae, BiocFileCache, BiocStyle, car, covr, cowplot,
e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls,
pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs
ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown,
tidyverse, knitr, ggbio, biovizBase,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue,
testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq,
splatter, scater, rnaseqcomp, biomaRt
HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite,
rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit,
testthat, digest
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
Hmisc, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>=
2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges,
SummarizedExperiment, rmarkdown
TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools,
testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges,
circlize, tictoc, IRanges, stats, SummarizedExperiment,
rmarkdown
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle, knitr
BiocStyle, knitr, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat
(>= 3.0.0), xml2
BiocStyle, knitr, rmarkdown, systemPipeRdata,
GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11)
testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr,
pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment,
glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>=
1.1.0), cicerone
systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>=
3.0.0), BiocGenerics, Biostrings, methods
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, rGREAT, SpectralTAD
tinytest, BiocStyle, ggimage, knitr, rmarkdown
testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer,
BiocStyle
testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS,
covr
BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra,
testthat (>= 3.0.0), covr
BiocStyle, caret, circlize, class, covr, dplyr, e1071,
glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC,
randomForest, rmarkdown, shiny, spelling, sva, testthat
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame,
AnnotationHub, ExperimentHub, pathview, clusterProfiler,
Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph,
supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter,
gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3),
scales, grid
testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2,
BiocStyle, animation, rmarkdown, pander
AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData,
ComplexHeatmap, devtools, dplyr, httr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr,
rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils,
testthat, TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>=
3.0.0)
BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr,
RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest
knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0)
knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2,
DESeq2, BiocGenerics, ggrepel, rcompanion,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, data.table, testthat, AnnotationFilter, Biobase,
GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors,
EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db,
GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR,
ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer,
rmarkdown
BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager,
Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva,
GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2,
widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot,
betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional,
survminer, tidySummarizedExperiment, markdown, uwot,
matrixStats, igraph, EGSEA
BiocStyle, testthat, knitr, markdown, SingleCellSignalR,
SingleR, scater, scran, tidyHeatmap, igraph, GGally, Matrix,
uwot, celldex, dittoSeq, EnsDb.Hsapiens.v86
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat
BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse,
igraph, gplots
BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db,
org.Mm.eg.db, testthat, rmarkdown
knitr, aroma.light, affxparser, RUnit, BiocGenerics
GenomicFeatures, shiny, BiocManager, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
BiocStyle, xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools,
PharmacoGx, xtable, markdown
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr,
htmltools, rmarkdown, motifStack
knitr, rmarkdown, testthat, covr, clusterExperiment
BiocNeighbors, DelayedArray, DelayedMatrixStats,
BiocParallel, testthat, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
testthat, TENxPBMCData, scran, knitr, rmarkdown
testthat, roxygen2, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, inline, parallel
scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors,
rmarkdown, knitr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr
knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
tibble, tidyr, SingleCellExperiment
RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR,
markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Athaliana.TAIR.TAIR9
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats,
cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer
BiocStyle, knitr, rmarkdown, testthat, ggplot2,
BSgenome.Scerevisiae.UCSC.sacCer3
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways
knitr, testthat, scuttle, scran, metapod, BiocParallel,
BiocNeighbors, batchelor
fgsea, knitr, testthat, reticulate, rmarkdown
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
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown,
testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
BSgenome.Scerevisiae.UCSC.sacCer3
knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
DESeq2, fishpond, edgeR, limma, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, eds
Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2,
BiocStyle, knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
tidyr, testthat
BiocStyle, knitr, testthat, rmarkdown, dplyr
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, BiocParallel, seqLogo, motifStack, dplyr, ape,
ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
GenomicRanges, SummarizedExperiment, InteractionSet,
testthat, knitr, rmarkdown, BiocStyle
SC3, knitr, testthat, reticulate, rmarkdown
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics,
r2glmm, readr
RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle
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
RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>=
1.21.3)
SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran,
scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot,
GGally, patchwork, metR
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
BiocSingular, BiocStyle, cowplot, dbscan, ExperimentHub,
hexbin, knitr, rmarkdown, scater, scattermore, scran, SFEData,
sparseMatrixStats, testthat (>= 3.0.0), vdiffr
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle,
clusterProfiler
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BiocStyle, knitr, rmarkdown,
IlluminaHumanMethylationEPICmanifest, irlba,
FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
knitr, rmarkdown, biomaRt, GenomicFeatures, testthat,
ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi,
AnnotationFilter
MSnbase, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown,
multtest, MALDIquant, pheatmap, Spectra (>= 1.1.17),
MsBackendMgf, progress, signal
BiocStyle, knitr, rmarkdown, markdown, testthat,
BSgenome.Hsapiens.UCSC.hg38, pander
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr,
pkgload, rmarkdown, rhdf5, scRNAseq, spelling, testthat, withr
BiocStyle, BiocGenerics, knitr, pander, rmarkdown,
tweeDEseqCountData, edgeR, kableExtra, RUnit
knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2
rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb,
profileplyr, rtracklayer, grid
BioPlex, biscuiteerData, bodymapRat, CLLmethylation,
CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP,
curatedMetagenomicData, curatedTCGAData, DMRcatedata,
DuoClustering2018, easierData, emtdata, epimutacionsData,
FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015,
GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets,
mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas,
MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr,
restfulSEData, RLHub, sesameData, SimBenchData,
SingleCellMultiModal, SingleMoleculeFootprintingData,
spatialDmelxsim, STexampleData, TabulaMurisData,
TabulaMurisSenisData, TENxVisiumData, tissueTreg,
VectraPolarisData, xcoredata
doMC, doMPI, doSNOW, doParallel, doRedis
parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
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