rMAT

rMAT is a software tool designed to identify regions enriched for transcription factor binding sites in Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) experiments on Affymetrix tiling arrays. The technique of ChIP-chip has become increasingly popular for studying DNA-protein binding or post-translational chromatin/histone modifications at the genomic level. However, the raw microarray intensities generate a vast amount of data that require sophisticated analysis algorithms and statistical methods to identify enriched regions accurately.

rMAT is an open-source R package that provides fast, free, and powerful analysis algorithms and statistical methods to identify enriched regions in ChIP-chip experiments on Affymetrix tiling arrays.