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DOI: 10.18129/B9.bioc.rtracklayer    

R interface to genome browsers and their annotation tracks

Bioconductor version: Release (3.5)

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>

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


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PDF R Script rtracklayer
PDF   Reference Manual
Text   NEWS


biocViews Annotation, DataImport, Software, Visualization
Version 1.36.6
In Bioconductor since BioC 2.2 (R-2.7) (9.5 years)
License Artistic-2.0 + file LICENSE
Depends R (>= 3.3), methods, GenomicRanges(>= 1.21.20)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.13.8), S4Vectors(>= 0.13.13), IRanges(>= 2.3.7), XVector(>= 0.9.4), GenomeInfoDb(>= 1.3.14), Biostrings(>= 2.43.7), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.17.8), GenomicAlignments(>= 1.5.4), tools
LinkingTo S4Vectors, IRanges, XVector
Suggests BSgenome(>= 1.33.4), humanStemCell, microRNA(>= 1.1.1), genefilter, limma,, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
Depends On Me BSgenome, ChIPComp, CoverageView, cummeRbund, EatonEtAlChIPseq, exomePeak, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, MethylSeekR, r3Cseq, regioneR, RIPSeeker, spliceR
Imports Me AnnotationHubData, annotatr, ATACseqQC, ballgown, BiSeq, branchpointer, BSgenome, CAGEr, casper, CexoR, chipenrich,, ChIPseeker, ChromHeatMap, CNEr, coMET, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, DeepBlueR, derfinder, diffloop, ensembldb, erma, FourCSeq, FunciSNP,, genbankr, geneAttribution, geneLenDataBase, genomation, GenomicFeatures, GenomicInteractions, genotypeeval, ggbio, GGtools, gmapR, GOTHiC, gQTLBase, GreyListChIP, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, karyoploteR, MADSEQ, MEDIPS, metagene, methyAnalysis, methylKit, motifbreakR, MotifDb, NADfinder, normr, Pbase, PGA, proBAMr, PureCN, qsea, QuasR, RCAS, recount, recoup, regioneR, Repitools, RiboProfiling, RNAprobR, roar, seqplots, SGSeq, soGGi, SVM2CRM, TFBSTools, trackViewer, transcriptR, TSRchitect, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me alpine, AnnotationHub, BiocFileCache, biovizBase, ChIPpeakAnno, CINdex, compEpiTools, CrispRVariants, dsQTL, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, GeuvadisTranscriptExpr, goseq, InPAS, interactiveDisplay, metaseqR, methylumi, MotIV, MutationalPatterns, NarrowPeaks, oneChannelGUI, OrganismDbi, PasillaTranscriptExpr, PICS, PING, pqsfinder, R453Plus1Toolbox, Ringo, rMAT, RnBeads, RSVSim, signeR, similaRpeak, triplex, TSSi, TVTB
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