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


BACKGROUND
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.
Droit
Arnaud
A
Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada. arnaud.droit@ircm.qc.ca
Cheung
Charles
C
Gottardo
Raphael
R
D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D030541:Databases, Genetic; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000737:chemistry
D014157:Transcription Factors