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

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ChIP-seq analysis workflow schema

ChIP sequencing data analysis bioinformatics software tools

Most Recent Tools

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dictyExpress
Web

dictyExpress

Enables the broad adoption of next generation sequencing (NGS) based inquiries.…

Enables the broad adoption of next generation sequencing (NGS) based inquiries. dictyExpress is a web application designed for exploration of transcriptomics datasets. It allows users to select among…

G T A T C G C T A
QReserve
Web

QReserve

Allows to collaborate and connect over equipment, services and other resources.…

Allows to collaborate and connect over equipment, services and other resources. QReserve is an online platform which permits users to manage their resources and equipment. This tool presents several…

G T A T C G C T A
FQC
Desktop

FQC

Facilitates quality control (QC) of FASTQ files. FQC combines a command line…

Facilitates quality control (QC) of FASTQ files. FQC combines a command line interface (CLI) depending on FastQC for processing FASTQ files, and a frontend website for plotting, styling and…

G T A T C G C T A
Index_investiga…
Desktop

Index_investigator

Tests if index switching is occurring in a given dataset. Index_investigator is…

Tests if index switching is occurring in a given dataset. Index_investigator is a script that provides a way to visualize switch for sequenced genomic datasets. This method shows that in samples,…

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.

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,…

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