From BITS wiki
- MACS, MACS2 to find peaks from mapping data.
- PeakAnalyzer (includes PeakSplitter & PeakAnnotator) from the Bertone Group at EBI.
- PeakZilla check this!
- SeqMonk, intuitive NGS analysis GUI from the Babraham Bioinformatics group.
- SICER from 'A clustering approach for identification of enriched domains from histone modification ChIP-Seq data' by Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao and Weiqun Peng.
- Homer, standing for Hypergeometric Optimization of Motif EnRichment, is a suite of tools for Motif Discovery and next-gen sequencing analysis
- ChipSeek integrates several analyses into one WEB ChIP-Seq workflow.
- The Motif Enrichment Tool ( MET ) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif ().
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