rtracklayer

R interface to genome browsers and their annotation tracks

Extensible framework for interacting with multiple genome browsers (currently UCSC and Argo built-in) and manipulating annotation tracks in various formats (currently GFF, BED 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
Maintainer Michael Lawrence

To install this package, start R and enter:

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

Documentation

Package Downloads
rtracklayer
Reference Manual
Package source rtracklayer_1.2.2.tar.gz
Windows binary rtracklayer_1.2.2.zip
MacOS X 10.4 (Tiger) binary rtracklayer_1.2.2.tgz
MacOS X 10.5 (Leopard) binary rtracklayer_1.2.2.tgz
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Details

biocViews
Annotation , Visualization
Depends
R , Biobase , methods , RCurl
Imports
XML , rJava , IRanges , Biostrings
Suggests
humanStemCell , microRNA , genefilter , limma , org.Hs.eg.db
System Requirements
License Artistic-2.0
URL
Depends On Me
GGtools
Imports Me
Suggests Me
Development History Bioconductor Changelog