ChIP-seq の Peak calling tool を集めたよ

ほかにもあったら教えてください。プログラム/プロジェクト名がツールのプロジェクトサイトへのリンク。その論文タイトルは論文へのリンクになっています。

ツール名の50音順です。

• CCCT - A signal–noise model for significance analysis of ChIP-seq with negative control, chipdiff と同じグループ


• CisGenome - CisGenome: An integrated software system for analyzing ChIP-chip and ChIP-seq data.


• ChromSig - ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.


• ChIPDiff - An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data


• ChIP-Seq Analysis Server


• FindPeaks - FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Version 4.0 is out.


• GLITR - Extracting transcription factor targets from ChIP-Seq data


• HPeak - HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data


• MACS - Model-based Analysis of ChIP-Seq (MACS).


• PeakSeq - PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

• PoissonMixtureModel - http://www.biomedcentral.com/1471-2164/9/S2/S23


• QuEST - Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data


• TIROE - An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network


• Useq - Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks


• WTD/MSP/MTC - Design and analysis of ChIP-seq experiments for DNA-binding proteins