ChIP sequencing data analysis bioinformatics software tools

ChIP-seq analysis steps

Read pre-processing

Data analysis

Visualization & interpretation

File, data & workflows

ChIP-seq analysis workflow

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ChIP-seq analysis 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,…

ChIP sequencing data analysis bioinformatics software tools

Most Recent Tools

Desktop app
G T A T C G C T A HMCan-diff HMCan-diff

HMCan-diff

Aims to detect differences in histone mark profiles between samples with…

Aims to detect differences in histone mark profiles between samples with significant genomic discrepancies. HMCan-diff is designed to analyze ChIP-seq data to detect changes in histone modifications…

Desktop app
G T A T C G C T A Expression in a… Expression in a Rate-Normalized GEne Specific

EXRANGES Expression in a Rate-Normalized GEne Specific

Adjusts how expression data is provided to the network algorithm. ExRANGES…

Adjusts how expression data is provided to the network algorithm. ExRANGES prioritizes targets differently than traditional expression and improves the ability of these networks to accurately predict…

Desktop app
G T A T C G C T A MotifCatcher MotifCatcher

MotifCatcher

An integrated framework for motif discovery. MotifCatcher extends the…

An integrated framework for motif discovery. MotifCatcher extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences…

Desktop app
G T A T C G C T A Pique Pique

Pique

Identifies protein–DNA binding events in small bacterial and archaeal…

Identifies protein–DNA binding events in small bacterial and archaeal genomes. Pique integrates with the Gaggle toolkit to facilitate downstream data visualization, curation and analysis. It also…

Most Popular Tools

Desktop app
G T A T C G C T A Hypergeometric… Hypergeometric Optimization of Motif EnRichment

HOMER Hypergeometric Optimization of Motif EnRichment

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

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…

Desktop app
G T A T C G C T A NGS-QC Generator NGS-QC Generator

NGS-QC Generator

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

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

Desktop app
G T A T C G C T A kmerHMM kmerHMM

kmerHMM

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

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

Desktop app
G T A T C G C T A phantompeakqualtools phantompeakqualtools

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. It can also be used to obtain robust estimates of the predominant fragment…

Curators for ChIP-seq analysis

  • Hélène Dauchel's avatar image
    Hélène Dauchel
    LITIS EA 4108 Computer science,…
  • Julie Dubois-Chevalier's avatar image
    Julie Dubois-Chevalier
    INSERM UMR1011, University of…
  • Fabien Pichon's avatar image
    Fabien Pichon
    Laboratory for Epigenetics and…

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