Main logo
?

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

Data preprocessing

Data processing

Data analysis

Annotation

Interpretation

Data visualization

Pipelines & Utilities

ChIP-seq analysis workflow

Click the icons of the schema to view tools

ChIP-seq analysis workflow schema

Experts in ChIP-seq analysis

They share and annotate bioinformatics tools

  • Julie Dubois-Chevalier's avatar image
    Julie Dubois-Chevalier
    INSERM UMR1011, University of Lille-Nord de France, University Lille 2, Institut Pasteur de Lille and European Genomic Institute for Diabetes (EGID) FR 3508, Lille, France
  • Fabien Pichon's avatar image Fabien Pichon's country flag
  • Hélène Dauchel's avatar image
    Hélène Dauchel
    LITIS EA 4108 Computer science, information processing and systems laboratory, Rouen, France

Most recent bioinformatics tools

G T A T C G C T A
TRUmiCount
Algorithm

TRUmiCount

Removes the biases inherent in raw Unique Molecular Identifier (UMI) counts and…

Removes the biases inherent in raw Unique Molecular Identifier (UMI) counts and produces unbiased and low-noise measurements of transcript abundance. In these conditions, TRUmiCount can realize…

G T A T C G C T A
NucBase
Desktop

NucBase

Aligns short reads from large nucleic acid databases to reference sequences or…

Aligns short reads from large nucleic acid databases to reference sequences or genomes. NucBase computes the Burrows-Wheeler Transform (BWT) of the target, as well as its suffix array to proceed. It…

G T A T C G C T A
LIBSVM
Desktop

LIBSVM

Supports vector classification, regression and distribution estimation. LIBSVM…

Supports vector classification, regression and distribution estimation. LIBSVM solves C-SVM classification, nu-SVM classification, one-class-SVM, epsilon-SVM regression, and nu-SVM regression. It…

G T A T C G C T A
PyBrain
Desktop

PyBrain

Facilitates both the application of and research on premier learning…

Facilitates both the application of and research on premier learning algorithms. PyBrain is a machine learning library that implements many recent learning algorithms and architectures ranging from…

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
Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

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…

ZENBU
Web

ZENBU

Enables data exploration through "on-demand" data processing and…

Enables data exploration through "on-demand" data processing and interactive linked-visualizationsthus enabling concurrent views from the same mere primary sequence alignment data which…

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