ChIP-seq analysis steps

Preprocessing & quality control

Data analysis

Visualization & interpretation

File, data & workflows

ChIP-seq analysis workflow

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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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BOLD
Web

BOLD Barcode of Life Data Systems

Aides the acquisition, storage, analysis and publication of DNA barcode…

Aides the acquisition, storage, analysis and publication of DNA barcode records. BOLD is a cloud-based data storage and analysis platform which consists of four main modules: a data portal, an…

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BioContainers
Desktop

BioContainers

Allows labs of all sizes to easily install bioinformatics software, maintain…

Allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on…

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ZBIT…
Web

ZBIT Bioinformatics Toolbox

Provides web-based access to a collection of bioinformatics tools developed for…

Provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. ZBIT Bioinformatics Toolbox is designed to…

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GenomeZip
Desktop

GenomeZip

Compress human genomes based on entropy coding, using a reference genome and…

Compress human genomes based on entropy coding, using a reference genome and known Single Nucleotide Polymorphisms (SNPs). GenomeZip also explores several intrinsic features of genomes and…

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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