CEAS: Cis-regulatory Element Annotation System

This is a tool 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.

A recommended package to install is R.