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Bioinformatics. 2010 Mar 1;26(5):678-9. doi: 10.1093/bioinformatics/btq023. Epub 2010 Jan 19.

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

Author information

1
Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada. arnaud.droit@ircm.qc.ca

Abstract

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.

PMID:
20089513
DOI:
10.1093/bioinformatics/btq023
[Indexed for MEDLINE]
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