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Workflow/pipeline software tools | ChIP sequencing data analysis

These software pipelines automate ChIP sequencing analysis by combining a number of specific analysis programs together.

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SPP
Desktop

SPP

An R package for analysis of ChIP-seq and other functional sequencing data. SPP…

An R package for analysis of ChIP-seq and other functional sequencing data. SPP has been designed to detect protein binding positions with high accuracy. SPP can also examine the saturation level of…

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CisGenome
Desktop

CisGenome

An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory…

An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.

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cERMIT
Desktop

cERMIT conserved Evidence-Ranked Motif Identification Tool

Allows motif identification. cERMIT is designed to analyze current large…

Allows motif identification. cERMIT is designed to analyze current large genomic regulatory datasets such as those from ChIPchip or ChIP-seq experiments. The software makes use of the complete data…

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Cistrome
Web

Cistrome

A web-based application called Cistrome, based on the Galaxy open source…

A web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major…

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RUbioSeq
Desktop

RUbioSeq

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq…

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq,…

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seqMINER
Desktop

seqMINER

Allows comparison and integration of multiple ChIP-seq datasets and extraction…

Allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. seqMINER can handle the biological complexity of most experimental…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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ChIP-seq
Desktop
Web

ChIP-seq

Provides access to a set of useful tools performing common ChIP-Seq data…

Provides access to a set of useful tools performing common ChIP-Seq data analysis tasks. The ChIP-Seq Web Server also includes positional correlation analysis, peak detection, and genome partitioning…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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ChiLin
Desktop

ChiLin

Automates quality controls and data analyses on ChIP-seq and DNase-seq data.…

Automates quality controls and data analyses on ChIP-seq and DNase-seq data. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over…

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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique…

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PRI-CAT
Web

PRI-CAT Plant Research International ChIP-seq analysis tool

Allows to manage and analyse ChIP-seq experiments. PRI-CAT focuses on plants…

Allows to manage and analyse ChIP-seq experiments. PRI-CAT focuses on plants and particularly on Arabidopsis CHIP-seq analysis. It uses the ratio between the number of mapped reads in experimental…

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ChIPseeqer
Desktop

ChIPseeqer

Enables broad and analysis of ChIP-seq data. ChIPseeqer is a comprehensive…

Enables broad and analysis of ChIP-seq data. ChIPseeqer is a comprehensive computational framework that includes: (1) gene-level annotation of peaks, (2) pathways enrichment analysis, (3) regulatory…

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Nebula
Web

Nebula

A web service provided by Institut Curie and powered by Galaxy which allows…

A web service provided by Institut Curie and powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.

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CIPHER
Desktop

CIPHER

Automates the processing and analysis of several commonly used Next Generation…

Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease…

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Workflow_of_ChI…
Desktop

Workflow_of_ChIPSeq

Provides a ChIP-Seq data analysis pipeline that performs all the essential…

Provides a ChIP-Seq data analysis pipeline that performs all the essential steps in one script. Workflow_of_CHIPSeq aims to help biologists with few bioinformatics skills in their analysis of…

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ChiPSeqFPro
Desktop

ChiPSeqFPro ChIP-Seq Full Processing

Automates processing of a collection of ChIPSeq or ATAC-Seq data starting from…

Automates processing of a collection of ChIPSeq or ATAC-Seq data starting from the gzip compressed fastq files. ChIPSeqFPro is a pipeline that performs the quality control using FastQC, mapping to…

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Bio-Docklets
Desktop

Bio-Docklets

Aims to perform basic analysis and interpretation of datasets with minimal…

Aims to perform basic analysis and interpretation of datasets with minimal effort. Bio-Docklets is an approach for abstracting the complex data operations of multi-step, bioinformatics pipelines for…

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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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ChIPSeqWorkflow…
Desktop

ChIPSeqWorkflows

A set of 20 ChIP-seq analysis software modules implemented in the Kepler…

A set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full…

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QuickNGS
Desktop
Web

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple…

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…

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ChIPQC
Desktop

ChIPQC

Computes quality metrics for aligned data from ChIP-seq experiments. ChIPQC…

Computes quality metrics for aligned data from ChIP-seq experiments. ChIPQC will automatically compute several quality metrics, and provides simple ways to generate a ChIP- seq experiment quality…

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Crunch
Web

Crunch

A completely automated procedure for ChIP-seq data analysis, starting from raw…

A completely automated procedure for ChIP-seq data analysis, starting from raw read quality control, through read mapping, peak detection and annotation, and including comprehensive DNA sequence…

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Pyicos
Desktop

Pyicos

Analyses mapped reads from diverse High-throughput sequencing (HTS)…

Analyses mapped reads from diverse High-throughput sequencing (HTS) experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. Pyicos is a command line utility for the…

W-ChIPeaks
Web

W-ChIPeaks

A comprehensive web application tool for processing ChIP-chip and ChIP-seq…

A comprehensive web application tool for processing ChIP-chip and ChIP-seq data. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on…

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HiChIP
Desktop

HiChIP

A comprehensive analysis pipeline that can be configured to analyze ChIP-Seq…

A comprehensive analysis pipeline that can be configured to analyze ChIP-Seq data derived from varying antibodies and experiment designs.

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chipseq
Desktop

chipseq

Helps to process short read data for chipseq experiments. chiseq provides a…

Helps to process short read data for chipseq experiments. chiseq provides a function that plots one or two coverage vectors over a relatively small interval in the genome. It can identify and produce…

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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CAST
Desktop

CAST Chip-Seq Analysis System Tool

Identifies protein binding positions with high accuracy. CAST can be useful in…

Identifies protein binding positions with high accuracy. CAST can be useful in analysis of microarray alternative such as ChIP-chip.

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