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: 2.14

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	1.24.2
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, casper, CexoR, ChIPseeker, 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 Archives

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

Package Source	rtracklayer_1.24.2.tar.gz
Windows Binary	rtracklayer_1.24.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	rtracklayer_1.24.2.tgz
Mac OS X 10.9 (Mavericks)	rtracklayer_1.24.2.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Oligonucleotide Arrays
High-throughput Sequencing
Counting Reads for Differential Expression (parathyroideSE vignette)
Annotation
Annotating Variants
Annotating Ranges
Flow Cytometry and other assays
Candidate Binding Sites for Known Transcription Factors
Cloud-enabled cis-eQTL search and annotation

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