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

rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.13

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>

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	1.22.7
In Bioconductor since	BioC 2.2 (R-2.7)
License	Artistic-2.0
Depends	R (>= 2.10), methods, GenomicRanges(>= 1.13.3)
Imports	XML (>= 1.98-0), BiocGenerics(>= 0.7.7), IRanges(>= 1.19.34), XVector(>= 0.1.3), GenomicRanges(>= 1.13.43), Biostrings(>= 2.29.18), BSgenome(>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.13.1)
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, exomePeak, HTSeqGenie, MethylSeekR, r3Cseq, RIPSeeker, spliceR
Imports Me	BiSeq, CAGEr, CexoR, ChromHeatMap, customProDB, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FunciSNP, FunciSNP.data, geneLenDataBase, GenomicFeatures, ggbio, gmapR, Gviz, HiTC, HTSeqGenie, interactiveDisplay, MEDIPS, methyAnalysis, MotifDb, VariantAnnotation, 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 Archives

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

Package Source	rtracklayer_1.22.7.tar.gz
Windows Binary	rtracklayer_1.22.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	rtracklayer_1.22.7.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats