rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: Development (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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("rtracklayer")

Documentation

PDF R Script rtracklayer
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, Software, Visualization
Version 1.25.1
In Bioconductor since BioC 2.2 (R-2.7)
License Artistic-2.0
Depends R (>= 2.10), methods, GenomicRanges(>= 1.15.26)
Imports XML (>= 1.98-0), BiocGenerics(>= 0.7.7), IRanges(>= 1.19.34), XVector(>= 0.1.3), GenomicRanges(>= 1.15.26), Biostrings(>= 2.29.18), BSgenome(>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.13.1), GenomicAlignments, tools
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
URL
Depends On Me CoverageView, cummeRbund, EatonEtAlChIPseq, exomePeak, GenomicFiles, MethylSeekR, r3Cseq, RIPSeeker, spliceR
Imports Me BiSeq, CAGEr, CexoR, ChromHeatMap, CNEr, CompGO, customProDB, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FunciSNP, FunciSNP.data, geneLenDataBase, GenomicFeatures, ggbio, GGtools, gmapR, GOTHiC, Gviz, gwascat, HiTC, HTSeqGenie, MEDIPS, methyAnalysis, MotifDb, roar, TFBSTools, trackViewer, VariantAnnotation, VariantTools
Suggests Me biovizBase, FDb.FANTOM4.promoters.hg19, GenomicAlignments, GenomicRanges, ggtut, goseq, ind1KG, interactiveDisplay, metaseqR, methylumi, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, QuasR, R453Plus1Toolbox, Repitools, Ringo, rMAT, RSVSim, triplex, TSSi

Package Downloads

Package Source rtracklayer_1.25.1.tar.gz
Windows Binary rtracklayer_1.25.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rtracklayer_1.25.1.tgz
Mac OS X 10.9 (Mavericks)
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