rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.7

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, and WIG 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

Details

biocViews Annotation, Visualization, DataImport
Depends R (>= 2.7.0), methods, RCurl (>= 1.4-2)
Imports XML (>= 1.98-0), IRanges(>= 1.8.7), GenomicRanges(>= 1.1.34), Biostrings(>= 2.15.22), BSgenome(>= 1.15.17)
Suggests humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19
System Requirements
License Artistic-2.0
URL
Depends On Me EatonEtAlChIPseq, GGtools
Imports Me ChromHeatMap, geneLenDataBase, GenomicFeatures, GGtools, R453Plus1Toolbox
Suggests Me GenomicFeatures, GGtools, ind1KG, MotIV, oneChannelGUI, PICS, R453Plus1Toolbox, Ringo, rMAT
Version 1.10.6
Since Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source rtracklayer_1.10.6.tar.gz
Windows Binary rtracklayer_1.10.6.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary rtracklayer_1.10.6.tgz
Package Downloads Report Download Stats

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