ChIP sequencing data analysis bioinformatics software tools

ChIP-seq analysis steps

Preprocessing & quality control

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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Ketrew
Desktop

Ketrew

Provides an EDSL API to define complex and convoluted workflows…

Provides an EDSL API to define complex and convoluted workflows ((interdependent steps/programs using a lot of data, with many parameter variations, running on different hosts with various…

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chipseq
Desktop

chipseq

Helps to process short read data for chipseq experiments. chiseq provides a…

Helps to process short read data for chipseq experiments. chiseq provides a function that plots one or two coverage vectors over a relatively small interval in the genome. It can identify and produce…

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epic
Desktop

epic

Finds medium to diffusely enriched domains in chip-seq data. epic is a fast,…

Finds medium to diffusely enriched domains in chip-seq data. epic is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm. It can use one core per…

SUPERmerge
Desktop

SUPERmerge

Allows the analysis and annotation of coverage islands within individual read…

Allows the analysis and annotation of coverage islands within individual read alignment (BAM) files of histone modification ChIPseq datasets harboring broad chromatin domains. SUPERmerge allows…

Most Popular Tools

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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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.

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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