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ChIP sequencing software tools

High-throughput sequencing software tools

ChIP-seq applications

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ChIP-seq workflow schema

Chromatin immunoprecipitation followed by sequencing (ChIP-seq), first described in 2007 (Barski et al., 2007; Johnson et al., 2007; Mikkelsen et al., 2007; Robertson et al., 2007), allows in vivo determination of where a protein binds the genome, which can be transcription factors, DNA-binding enzymes, histones, chaperones, or nucleosomes (Park, 2009; Furey, 2012).
Curators: Julie Dubois-Chevalier and Fabien Pichon

ChIP-seq Curators
Hélène Dauchel avatar
Hélène Dauchel
Julie Dubois-Chevalier avatar
Julie Dubois-Chevalier
Fabien Pichon avatar
Fabien Pichon

Most Recent Tools

new
OMIC_12446
Interpretation

Heat*seq

A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq,…

A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise their sequencing data with respect to vast…

new
OMIC_12440
Interpretation

Chromatin Analysis and Exploration
ChAsE

A cross-platform desktop application developed for interactive visualization, exploration…

A cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and…

new
OMIC_12439
Interpretation

Epiviz

An interactive visualization tool for functional genomics data. Epiviz supports genome…

An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied…

new
OMIC_12434
Workflows/pipelines

ChIPSeqWorkflows

A set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system;…

A set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The…

Most Popular Tools

popular
OMIC_00483
Motif discovery

Hypergeometric Optimization of Motif EnRichment
HOMER

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

popular
OMIC_00430
Quality control

NGS-QC Generator

A computational-based approach that infers quality indicators from the distribution of…

A computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.

popular
OMIC_02662
Motif discovery

kmerHMM

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and…

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation.

popular
OMIC_00431
Quality control

phantompeakqualtools

Computes quick but highly informative enrichment and quality measures for…

Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.

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