MACS

Model-based analysis of ChIP-Seq

http://liulab.dfci.harvard.edu/MACS/

ChIPseeqer

in-depth analysis of ChIP-seq datasets

http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/ChIPseeqer-2.0.tar.gz

HPeak

A HMM-based algorithm for defining read enriched regions

www.sph.umich.edu/csg/qin/HPeak

CASSys

ChIP-seq data Analysis Software System

http://localness.zbh.uni-hamburg.de/~ProjektChipSeq/cgi-bin/login.rb

PeakSeq

A general scoring approach for ChIP-seq data analysis.

http://info.gersteinlab.org/PeakSeq

Sole-Search

Integrated peak-calling and analysis software

http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi

SISSRS

Precise identification of binding sites from short reads generated from ChIP-Seq experiment

http://sissrs.rajajothi.com/

BayesPeak

Bayesian analysis of ChIP-seq data

http://bioconductor.org/packages/release/bioc/html/BayesPeak.html

PeakRanger

http://www.modencode.org/software/ranger/

FindPeaks 3.1

A tool for identifying areas of
enrichment

http://www.bcgsc.ca/platform/bioinfo/software/findpeaks

Sole-Search

An integrated analysis program for peak detection and functional annotation using ChIP-seq data

http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi

PeakAnalyzer

Genome-wide annotation of chromatin binding and modification loci

http://www.bioinformatics.org/peakanalyzer/wiki/

chromaSig

A Probabilistic Approach to Finding Common Chromatin Signatures

http://bioinformatics-renlab.ucsd.edu/rentrac/wiki/ChromaSig

Fish the ChIPs

A pipeline for automated genomic
annotation of ChIP-Seq data

http://bio.ifom-ieo-campus.it/ftc/