R interface to genome browsers and their annotation tracks

Bioconductor version: Release (2.11)

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>

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PDF R Script rtracklayer
PDF   Reference Manual
Text   NEWS


biocViews Annotation,Visualization,DataImport, Software
Version 1.18.2
In Bioconductor since BioC 2.2 (R-2.7)
License Artistic-2.0
Depends R (>= 2.10), methods, GenomicRanges(>= 1.9.6)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.1.0), IRanges(>= 1.15.37), GenomicRanges, Biostrings(>= 2.25.6), BSgenome(>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.7.3)
Suggests humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db
System Requirements
Depends On Me cummeRbund, EatonEtAlChIPseq, FDb.InfiniumMethylation.hg19, r3Cseq
Imports Me ChromHeatMap, FDb.InfiniumMethylation.hg19, FunciSNP.data, geneLenDataBase, GenomicFeatures, ggbio, gmapR, Gviz, HTSeqGenie, methyAnalysis, MotifDb, R453Plus1Toolbox
Suggests Me biovizBase, FDb.FANTOM4.promoters.hg19, GenomicFeatures, GenomicRanges, ggtut, gwascat, ind1KG, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, R453Plus1Toolbox, Ringo, rMAT, TSSi

Package Downloads

Package Source rtracklayer_1.18.2.tar.gz
Windows Binary rtracklayer_1.18.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) rtracklayer_1.18.2.tgz
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