To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")

In most cases, you don't need to download the package archive at all.

rtracklayer

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.

R interface to genome browsers and their annotation tracks

Bioconductor version: 3.3

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")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")

Documentation

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

browseVignettes("rtracklayer")

PDF	R Script	rtracklayer
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, DataImport, Software, Visualization
Version	1.32.2
In Bioconductor since	BioC 2.2 (R-2.7) (8.5 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(>= 0.9.33), IRanges(>= 2.3.7), XVector(>= 0.9.4), GenomeInfoDb(>= 1.3.14), Biostrings(>= 2.37.1), 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, org.Hs.eg.db, hgu133plus2.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
Depends On Me	BSgenome, ChIPComp, CoverageView, cummeRbund, EatonEtAlChIPseq, exomePeak, GenomicFiles, groHMM, Guitar, IdeoViz, MethylSeekR, r3Cseq, regioneR, RIPSeeker, spliceR
Imports Me	AnnotationHubData, ballgown, BiSeq, BSgenome, CAGEr, casper, CexoR, ChIPseeker, ChromHeatMap, CNEr, coMET, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, derfinder, ensembldb, erma, FourCSeq, FunciSNP, FunciSNP.data, genbankr, geneLenDataBase, genomation, GenomicFeatures, GenomicInteractions, genotypeeval, ggbio, GGtools, gmapR, GOTHiC, gQTLBase, GreyListChIP, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, MEDIPS, metagene, methyAnalysis, motifbreakR, MotifDb, Pbase, PGA, proBAMr, QuasR, recoup, regioneR, Repitools, RiboProfiling, RNAprobR, roar, seqplots, SGSeq, similaRpeak, soGGi, SVM2CRM, TFBSTools, trackViewer, transcriptR, VariantAnnotation, VariantTools, wavClusteR
Suggests Me	AnnotationHub, biovizBase, ChIPpeakAnno, CINdex, compEpiTools, CrispRVariants, dsQTL, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, GeuvadisTranscriptExpr, goseq, ind1KG, InPAS, interactiveDisplay, metaseqR, methylumi, MotIV, NarrowPeaks, oneChannelGUI, OrganismDbi, PasillaTranscriptExpr, PICS, PING, pqsfinder, R453Plus1Toolbox, Ringo, rMAT, RnBeads, RSVSim, triplex, TSSi
Build Report

Package Archives

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

Package Source	rtracklayer_1.32.2.tar.gz
Windows Binary	rtracklayer_1.32.2.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks)	rtracklayer_1.32.2.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/rtracklayer/tree/release-3.3
Package Short Url	http://bioconductor.org/packages/rtracklayer/
Package Downloads Report	Download Stats

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