Sidow Lab -
Quantitative Enrichment of Sequence Tags: QuEST QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from ChIP-seq experiments. Click here for Anton's QuEST site QuEST Downloads Software Package QuEST 2.4 (gzipped tar that includes readme, Oct 5 2009) QuEST test data (BIG FILES) GABP ChIP Data (gzipped text, 120.2 Mb, Mar 11 2008) Control (input) Dat
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite - BMC Systems Biology
ChIP-seq processing pipeline
This page last changed on January 28, 2016 by peterk. The page provides download links to an R package for processing ChIP-seq data. The rational behind most of the methods is described in the following paper: Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. Biotech. doi:10.1038/nbt.1508 version 1.13Download. SPP is now on Github! v
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https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0023
http://www.cs.ucr.edu/~stelo/papers/ISMB12.pdf
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures
ChIP-Seq
http://rsat.ulb.ac.be/
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data - BMC Bioinformatics
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Dynamic Regulatory Events Miner (DREM)
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data - BMC Bioinformatics
SIPeS - Site Identification from Paired-end Sequencing
https://academic.oup.com/bioinformatics/article-abstract/26/15/1864/189738
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls - Nature Biotechnology
Optimized detection of transcription factor-binding sites in ChIP-seq experiments
Optimized procedure for ChIP-seq peak detection
An integrated ChIP-seq analysis platform with customizable workflows - BMC Bioinformatics