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

G T A T C G C T A
Skyline…
Web

Skyline nucleosome browser

Offers a suite of many algorithms and programs for the identification of…

Offers a suite of many algorithms and programs for the identification of nucleosome peaks over the genome. The Skyline nucleosome browser is a web-based application that permits users can access…

G T A T C G C T A
PuFFIN
Desktop

PuFFIN Positioning for Fuzzy and FIxed Nucleosomes

Builds genome-wide nucleosome maps specifically designed to take advantage of…

Builds genome-wide nucleosome maps specifically designed to take advantage of paired-end reads. PuFFIN is a method to produce a higher number of detected nucleosomes. In contrast to other approaches…

G T A T C G C T A
ARSDA
Desktop

ARSDA Analyzing RNA-Seq Data

Alleviates the problem associated with storage, transmission and analysis of…

Alleviates the problem associated with storage, transmission and analysis of high-throughput sequencing (HTS) data. ARSDA can take as input .SRA files or .fastq files of many gigabytes, build an…

G T A T C G C T A
KBWS
Desktop
Web

KBWS Keio Bioinformatics Web Service

Provides an EMBASSY (EMBOSS associated software) package for accessing popular…

Provides an EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services. As an EMBOSS package, KBWS can be accessed from a number of graphical user interfaces…

Most Popular Tools

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

  • 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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