DOI: 10.18129/B9.bioc.rtracklayer  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: 3.17

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Author: Michael Lawrence, Vince Carey, Robert Gentleman

Maintainer: Michael Lawrence <michafla at gene.com>

Citation (from within R, enter citation("rtracklayer")):


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biocViews Annotation, DataImport, Software, Visualization
Version 1.60.1
In Bioconductor since BioC 2.2 (R-2.7) (15.5 years)
License Artistic-2.0 + file LICENSE
Depends R (>= 3.5.0), methods, GenomicRanges(>= 1.37.2)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.35.3), S4Vectors(>= 0.23.18), IRanges(>= 2.13.13), XVector(>= 0.19.7), GenomeInfoDb(>= 1.15.2), Biostrings(>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13)
LinkingTo S4Vectors, IRanges, XVector
Suggests BSgenome(>= 1.33.4), humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
Depends On Me BRGenomics, BSgenome, CAGEfightR, ChIPComp, CoverageView, CSSQ, cummeRbund, EatonEtAlChIPseq, ExCluster, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, liftOver, MethylSeekR, ORFhunteR, r3Cseq, sequencing, StructuralVariantAnnotation, svaNUMT, svaRetro
Imports Me AnnotationHubData, annotatr, APAlyzer, ASpediaFI, ATACseqQC, ballgown, BgeeCall, BindingSiteFinder, biscuiteer, BiSeq, branchpointer, BSgenome, BSgenomeForge, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, chromswitch, circRNAprofiler, cliProfiler, CNEr, coMET, compartmap, consensusSeekeR, contiBAIT, conumee, crisprDesign, customProDB, dasper, DeepBlueR, derfinder, DEScan2, diffHic, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, ELMER, enhancerHomologSearch, enrichTF, ensembldb, EpiCompare, epidecodeR, epigraHMM, epimutacions, erma, esATAC, exomePeak2, extraChIPs, factR, fcScan, FindIT2, FLAMES, genbankr, geneAttribution, geneLenDataBase, GeneStructureTools, genomation, GenomicFeatures, GenomicInteractions, GenomicState, genotypeeval, ggbio, gmapR, gmoviz, GOTHiC, GreyListChIP, Gviz, hiAnnotator, HiCDCPlus, HiTC, HTSeqGenie, icetea, igvR, INSPEcT, InTAD, IsoformSwitchAnalyzeR, karyoploteR, m6Aboost, MADSEQ, magpie, maser, MEDIPS, metagene, metagene2, metaseqR2, methrix, methylKit, motifbreakR, MotifDb, multicrispr, MungeSumstats, NADfinder, nearBynding, NoRCE, normr, NxtIRFcore, NxtIRFdata, ODER, OGRE, OMICsPCA, ORFik, PAST, periodicDNA, plyranges, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, RCAS, recount, recount3, recoup, regioneR, REMP, Repitools, RGMQL, RiboProfiling, ribosomeProfilingQC, rifi, rifiComparative, RIPAT, RLSeq, rmspc, RNAmodR, roar, scanMiRApp, SCANVIS, scDblFinder, scPipe, scRNAseqApp, scruff, seqCAT, seqpac, seqsetvis, sevenC, SGSeq, shinyepico, signeR, SigsPack, SingscoreAMLMutations, sitadela, soGGi, spatialLIBD, SpliceWiz, srnadiff, syntenet, TFBSTools, trackViewer, transcriptR, TRESS, tRNAscanImport, txcutr, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me alpine, AnnotationHub, autonomics, BiocFileCache, biovizBase, bsseq, chipseqDB, cicero, CINdex, compEpiTools, CrispRVariants, crisprViz, DAMEfinder, DiffBind, eisaR, epistack, EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3, epivizrChart, epivizrData, excluderanges, FDb.FANTOM4.promoters.hg19, fourDNData, geneXtendeR, GenomicAlignments, GenomicDistributions, GenomicInteractionNodes, GenomicRanges, GeuvadisTranscriptExpr, goseq, gwascat, HiCExperiment, HiContacts, InPAS, interactiveDisplay, megadepth, methylumi, miRBaseConverter, MutationalPatterns, NanoMethViz, nanotubes, OrganismDbi, PasillaTranscriptExpr, Pi, PICS, PING, pipeFrame, plotgardener, pqsfinder, ProteoDisco, R453Plus1Toolbox, RcisTarget, rGADEM, Ringo, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, RSVSim, similaRpeak, systemPipeR, systemPipeRdata, TAPseq, TCGAutils, triplex, tRNAdbImport, TVTB, xcore
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