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 3.2 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.

R interface to genome browsers and their annotation tracks

Bioconductor version: 3.2

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 rtracklayer
PDF Reference Manual
Text NEWS
Text LICENSE

Details

biocViews Annotation, DataImport, Software, Visualization
Version 1.30.4
In Bioconductor since BioC 2.2 (R-2.7) (8 years)
License Artistic-2.0 + file LICENSE
Depends R (>= 2.10), methods, GenomicRanges(>= 1.21.20)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.13.8), S4Vectors(>= 0.7.11), 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, epivizr, exomePeak, GenomicFiles, groHMM, Guitar, IdeoViz, MethylSeekR, r3Cseq, regioneR, RIPSeeker, spliceR
Imports Me AnnotationHubData, ballgown, BiSeq, BSgenome, CAGEr, casper, CexoR, ChIPseeker, ChromHeatMap, CNEr, coMET, CompGO, conumee, customProDB, derfinder, ensembldb, erma, FourCSeq, FunciSNP, FunciSNP.data, geneLenDataBase, genomation, GenomicFeatures, genotypeeval, ggbio, GGtools, gmapR, GOTHiC, gQTLBase, GreyListChIP, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, MEDIPS, metagene, methyAnalysis, motifbreakR, MotifDb, Pbase, PGA, proBAMr, QuasR, regioneR, Repitools, RiboProfiling, RNAprobR, roar, seqplots, SGSeq, similaRpeak, soGGi, SVM2CRM, TFBSTools, trackViewer, VariantAnnotation, VariantTools, wavClusteR
Suggests Me AnnotationHub, biovizBase, ChIPpeakAnno, compEpiTools, dsQTL, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, ggtut, goseq, ind1KG, InPAS, interactiveDisplay, metaseqR, methylumi, MotIV, NarrowPeaks, oneChannelGUI, OrganismDbi, PICS, PING, 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_1.30.4.tar.gz
Windows Binary rtracklayer_1.30.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rtracklayer_1.30.1.tgz
Mac OS X 10.9 (Mavericks) rtracklayer_1.30.4.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/rtracklayer/tree/release-3.2
Package Short Url http://bioconductor.org/packages/rtracklayer/
Package Downloads Report Download Stats

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