PePr is an analysis pipeline for ChIP-Seq experiments with biological replicates, written and available as python scripts. The program accounts for the variation among biological replicates and (optionally) peak locations relative to gene structure information using a mixture model. It can be used either to determine histone modifications or transcription factor binding versus control data, or for two group comparisons.
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PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.
Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.
Bioinformatics. 2014 Jun 3. pii: btu372.