| Package | Maintainer | Title |
|---|---|---|
| BayesPeak | Jonathan Cairns | Bayesian Analysis of ChIP-seq Data |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| chipseq | Biocore Team c/o BioC user list | chipseq: A package for analyzing chipseq data |
| ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| DESeq | Simon Anders | Digital gene expresion analysis based on the negative binomial distribution |
| MotIV | Eloi Mercier , Raphael Gottardo | Motif Identification and Validation |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| rGADEM | Arnaud Droit | de novo motif discovery |