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

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PAD
Desktop
Web

PAD Proximal And Distal

Identify chromatin immunoprecipitation of 104 DNA binding proteins in embryonic…

Identify chromatin immunoprecipitation of 104 DNA binding proteins in embryonic stem cell (ESC) lines co-localization at these respective regions. PAD was applied to characterize protein…

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THiCweed
Desktop

THiCweed

Offers both speed and accuracy in finding multiple motifs in large datasets.…

Offers both speed and accuracy in finding multiple motifs in large datasets. THiCweed achieves its combination of speed and accuracy without resorting to heuristics in scoring and without resorting…

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compEpiTools
Desktop

compEpiTools

Facilitates several typical operations related to the quantification of the…

Facilitates several typical operations related to the quantification of the sequencing signal in a set of genomic regions. compEpiTools provides a number of methods to score these data in regions of…

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SSA
Desktop
Web

SSA Submodular Selection of Assays

Chooses a diverse panel of genomic assays that leverages methods from…

Chooses a diverse panel of genomic assays that leverages methods from submodular optimization. SSA serves as a model for how submodular optimization can be applied to other discrete problems in…

Most Popular Tools

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HOMER
Desktop

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…

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NGS-QC…
Desktop

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.

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kmerHMM
Desktop

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.

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phantompeakqual…
Desktop

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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