DOI: 10.18129/B9.bioc.rtracklayer    

This is the development version of rtracklayer; for the stable release version, see rtracklayer.

R interface to genome annotation files and the UCSC genome browser

Bioconductor version: Development (3.7)

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")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script rtracklayer
PDF   Reference Manual
Text   NEWS


biocViews Annotation, DataImport, Software, Visualization
Version 1.39.9
In Bioconductor since BioC 2.2 (R-2.7) (10 years)
License Artistic-2.0 + file LICENSE
Depends R (>= 3.3), methods, GenomicRanges(>= 1.31.8)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.13), XVector(>= 0.19.7), GenomeInfoDb(>= 1.15.2), Biostrings(>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), tools
LinkingTo S4Vectors, IRanges, XVector
Suggests BSgenome(>= 1.33.4), humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
Depends On Me BSgenome, ChIPComp, ChIPSeqSpike, 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, chipenrich.data, ChIPseeker, ChromHeatMap, chromswitch, CNEr, coMET, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, DeepBlueR, derfinder, DEScan2, diffloop, DMCHMM, dmrseq, ensembldb, erma, esATAC, FourCSeq, FunciSNP, FunciSNP.data, genbankr, geneAttribution, geneLenDataBase, GeneStructureTools, genomation, GenomicFeatures, GenomicInteractions, genotypeeval, ggbio, GGtools, gmapR, GOTHiC, gQTLBase, GreyListChIP, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, IsoformSwitchAnalyzeR, karyoploteR, MACPET, MADSEQ, MEDIPS, metagene, methyAnalysis, methylKit, motifbreakR, MotifDb, NADfinder, normr, Pbase, PGA, proBAMr, PureCN, qsea, QuasR, RCAS, recount, recoup, regioneR, Repitools, RGMQL, RiboProfiling, RNAprobR, roar, seqplots, SGSeq, soGGi, srnadiff, SVM2CRM, TFBSTools, trackViewer, transcriptR, tRNAscanImport, TSRchitect, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr
Suggests Me alpine, AnnotationHub, BiocFileCache, biovizBase, ChIPpeakAnno, CINdex, compEpiTools, CrispRVariants, dsQTL, ELMER, epivizrData, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, GeuvadisTranscriptExpr, goseq, InPAS, interactiveDisplay, metaseqR, methylumi, miRBaseConverter, MotIV, MutationalPatterns, NarrowPeaks, OrganismDbi, PasillaTranscriptExpr, PICS, PING, pqsfinder, R453Plus1Toolbox, Ringo, rMAT, RnBeads, RSVSim, signeR, similaRpeak, triplex, TSSi, TVTB
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package rtracklayer_1.39.9.tar.gz
Windows Binary rtracklayer_1.39.9.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) rtracklayer_1.39.9.tgz
Source Repository git clone https://git.bioconductor.org/packages/rtracklayer
Package Short Url http://bioconductor.org/packages/rtracklayer/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: