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Bioinformatics Advance Access originally published online on May 25, 2009
Bioinformatics 2009 25(14):1841-1842; doi:10.1093/bioinformatics/btp328
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

rtracklayer: an R package for interfacing with genome browsers

Michael Lawrence 1,*, Robert Gentleman 1,* and Vincent Carey 2

1 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102 and 2 Channing Laboratory, Harvard Medical School, Boston, MA 02115, USA

* To whom correspondence should be addressed.


  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.

Contact: mflawren{at}fhcrc.org

Associate Editor: Dmitrij Frishman

Received on February 2, 2009; revised on April 29, 2009; accepted on May 15, 2009

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