rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: Release (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

To install this package, start R and enter:

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

Documentation

PDF

R Script

rtracklayer

Reference Manual

Details

biocViews	Annotation, Visualization, DataImport
Depends	R, methods, RCurl
Imports	XML, IRanges, GenomicRanges, Biostrings, BSgenome
Suggests	humanStemCell, microRNA, genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19
System Requirements
License	Artistic-2.0
URL
Depends On Me	GGtools
Imports Me	ChromHeatMap, GGtools, GenomicFeatures, R453Plus1Toolbox
Suggests Me	GGtools, GenomicFeatures, MotIV, PICS, R453Plus1Toolbox, Ringo, oneChannelGUI, rMAT
Version	1.10.6

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