rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: Release (2.12)

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	1.20.4
In Bioconductor since	BioC 2.2 (R-2.7)
License	Artistic-2.0
Depends	R (>= 2.10), methods, GenomicRanges(>= 1.11.12)
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
URL
Depends On Me	cummeRbund, EatonEtAlChIPseq, HTSeqGenie, MethylSeekR, r3Cseq, RIPSeeker
Imports Me	BiSeq, CAGEr, ChromHeatMap, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FunciSNP.data, geneLenDataBase, GenomicFeatures, ggbio, gmapR, Gviz, HiTC, HTSeqGenie, MEDIPS, methyAnalysis, MotifDb, R453Plus1Toolbox, VariantTools
Suggests Me	biovizBase, FDb.FANTOM4.promoters.hg19, GenomicFeatures, GenomicRanges, ggtut, goseq, Gviz, gwascat, HiTC, ind1KG, methylumi, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, QuasR, R453Plus1Toolbox, Repitools, Ringo, rMAT, RSVSim, triplex, TSSi

Package Downloads

Package Source	rtracklayer_1.20.4.tar.gz
Windows Binary	rtracklayer_1.20.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	rtracklayer_1.20.4.tgz
Package Downloads Report	Download Stats

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