Journal Article

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments

Arnaud Droit, Charles Cheung and Raphael Gottardo

in Bioinformatics

Volume 26, issue 5, pages 678-679
Published in print March 2010 | ISSN: 1367-4803
Published online January 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq023
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments

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Summary: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) has evolved as a popular technique to study DNA–protein binding or post-translational chromatin/histone modifications at the genomic level. However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions.

Results: We present a fast, free and powerful, open source R package, rMAT, that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays.

Availability: The R-package rMAT is available from the Bioconductor web site at http://bioconductor.org and runs on Linux, MAC OS and MS-Windows. rMAT is distributed under the terms of the Artistic Licence 2.0.

Contact: arnaud.droit@ircm.qc.ca; raphael.gottardo@ircm.qc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1295 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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