ChIP sequencing data analysis bioinformatics software tools

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…

ChIP-seq analysis steps

Preprocessing & quality control

Data analysis

Visualization & interpretation

File, data & workflows

ChIP-seq analysis workflow

Click the icons of the schema to view tools

ChIP-seq analysis workflow schema

Most recent bioinformatics tools

G T A T C G C T A
Sleipnir
Desktop

Sleipnir

Allows to manipulate and mine very large biological data collections for…

Allows to manipulate and mine very large biological data collections for computational functional genomics. Sleipnir can perform common tasks: microarray processing, Bayesian and support vector…

G T A T C G C T A
ChromBiSim
Desktop

ChromBiSim CHROMatin BIclustering SIMplified

Allows to calculate biclusters. ChromBiSim is based on binarized data matrix of…

Allows to calculate biclusters. ChromBiSim is based on binarized data matrix of gene expression data sets. It can run on any size of data including whole genome histone modification profiles…

G T A T C G C T A
WSMD
Desktop

WSMD Weakly-Supervised Motif Discovery

Identifies motifs from ChIP-seq datasets. WSMD allows “global” optimization…

Identifies motifs from ChIP-seq datasets. WSMD allows “global” optimization of position weight matrices (PWMs) in continuous space, thereby reducing the information loss of model representation…

G T A T C G C T A
PairMotifChIP
Desktop

PairMotifChIP

Processes large DNA data sets. PairMotifChIP is an efficient method for…

Processes large DNA data sets. PairMotifChIP is an efficient method for extracting pairs of I-mers. It obtains motifs by combining extracted I-mers based on clustering methods. The tool is able to…

Most popular analytical software

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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.

G T A T C G C T A
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

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

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.