To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("rtracklayer")

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

rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: Release (3.0)

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:

source("http://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

Details

biocViews Annotation, DataImport, Software, Visualization
Version 1.26.1
In Bioconductor since BioC 2.2 (R-2.7)
License Artistic-2.0
Depends R (>= 2.10), methods, GenomicRanges(>= 1.17.39)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.11.3), S4Vectors(>= 0.2.3), IRanges(>= 1.99.28), XVector(>= 0.5.8), GenomeInfoDb(>= 1.1.19), Biostrings(>= 2.33.14), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.17.8), GenomicAlignments(>= 1.1.16), tools
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
System Requirements
URL
Depends On Me BSgenome, CoverageView, cummeRbund, EatonEtAlChIPseq, ESNSTCC, exomePeak, GenomicFiles, groHMM, IdeoViz, metagene, MethylSeekR, r3Cseq, RIPSeeker, spliceR
Imports Me ballgown, BiSeq, BSgenome, CAGEr, casper, CexoR, ChIPseeker, ChromHeatMap, CNEr, CompGO, customProDB, derfinder, exonfindR, FourCSeq, FunciSNP, FunciSNP.data, geneLenDataBase, GenomicFeatures, GenomicInteractions, ggbio, GGtools, gmapR, GOTHiC, Gviz, gwascat, hiAnnotator, HiTC, HTSeqGenie, MEDIPS, methyAnalysis, MotifDb, proBAMr, Repitools, roar, seqplots, SGSeq, TFBSTools, trackViewer, VariantAnnotation, VariantTools, wavClusteR
Suggests Me biovizBase, compEpiTools, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, ggtut, goseq, ind1KG, interactiveDisplay, metaseqR, methylumi, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, QuasR, R453Plus1Toolbox, Ringo, rMAT, RSVSim, triplex, TSSi

Package Archives

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

Package Source rtracklayer_1.26.1.tar.gz
Windows Binary rtracklayer_1.26.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rtracklayer_1.26.1.tgz
Mac OS X 10.9 (Mavericks) rtracklayer_1.26.1.tgz
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