rtracklayer: an R package for interfacing with genome browsers

Abstract

SUMMARY: The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. The user may (i) transfer annotation tracks to and from a genome browser and (ii) create and manipulate browser views to focus on a particular set of annotations in a specific genomic region. Currently, the UCSC genome browser is supported. AVAILABILITY: The package is freely available from http://www.bioconductor.org/. A quick-start vignette is included with the package.