CEAS (Cis-regulatory Element Annotation System) is a standalone Python package for analyzing ChIP-chip/seq data. The tool was designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. As a stand-alone extension of our web application CEAS , it provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.
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Shin H, Liu T, Manrai AK, Liu XS.
CEAS: cis-regulatory element annotation system.
Bioinformatics. 2009 Oct 1;25(19):2605-6. Epub 2009 Aug 18.