rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.6

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, Biobase
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
Suggests Me	MotIV, PICS, Ringo, oneChannelGUI, rMAT
Version	1.8.1

Package Downloads

Package Source	rtracklayer_1.8.1.tar.gz
Windows Binary	rtracklayer_1.8.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	rtracklayer_1.8.1.tgz
Package Downloads Report	Download Stats