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Decision-support software tools | ChIP sequencing data analysis

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SignalSpider
Desktop

SignalSpider SignalSpider

A probabilistic model for deciphering the combinatorial genome-wide binding…

A probabilistic model for deciphering the combinatorial genome-wide binding patterns of DNA-binding proteins from normalized ChIP-Seq profiles.

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ISMARA
Web

ISMARA Integrated System for Motif Activity Response Analysis

A methodology that models gene expression or chromatin modifications in terms…

A methodology that models gene expression or chromatin modifications in terms of genome-wide predictions of regulatory sites and completely automated it into a web-based tool.

ChIPpeakAnno
Desktop

ChIPpeakAnno

Facilitates batch annotation of enriched peaks identified from ChIP-seq,…

Facilitates batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions.…

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MultiGPS
Desktop

MultiGPS

Analyses condition-specific binding events from multi-condition ChIP-seq data.…

Analyses condition-specific binding events from multi-condition ChIP-seq data. MultiGPS incorporates prior information into binding event discovery, allowing models of joint binding and sequence…

Epiviz
Web
Desktop

Epiviz

An interactive visualization tool for functional genomics data. Epiviz supports…

An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using…

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GATE
Desktop

GATE Genomic Annotation from Time-couse Epigenomic data

A model-based, open source tool for chromatin states prediction based on…

A model-based, open source tool for chromatin states prediction based on time-course Epigenetic marks data.

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MuSERA
Desktop

MuSERA Multiple Sample Enriched Region Assessment

A broadly useful standalone tool for both interactive and batch analysis of…

A broadly useful standalone tool for both interactive and batch analysis of combined evidence from enriched regions (ERs) in multiple ChIP-seq or DNase-seq replicates. Besides rigorously combining…

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ChAsE
Desktop

ChAsE Chromatin Analysis and Exploration

A cross-platform desktop application developed for interactive visualization,…

A cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close…

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Epigenomix
Desktop

Epigenomix

A package to detect genes that show different transcript abundances between two…

A package to detect genes that show different transcript abundances between two conditions putatively caused by alterations in histone modification. Epigenomix is based on a correlation measure for…

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ChromNet
Desktop

ChromNet

A statistical method, to infer a network of interactions among regulatory…

A statistical method, to infer a network of interactions among regulatory factors - transcription factors and histone modifications - co-localized at particular genomic regions, the chromatin…

SUPERmerge
Desktop

SUPERmerge

Allows the analysis and annotation of coverage islands within individual read…

Allows the analysis and annotation of coverage islands within individual read alignment (BAM) files of histone modification ChIPseq datasets harboring broad chromatin domains. SUPERmerge allows…

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Seq2pathway
Desktop

Seq2pathway

An R/Python wrapper for pathway (or functional gene-set) analysis of genomic…

An R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with…

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ChIPseeker
Desktop

ChIPseeker

Annotates ChIP-seq data analysis. ChIPseeker supports annotating ChIP peaks and…

Annotates ChIP-seq data analysis. ChIPseeker supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions.…

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DChIPRep
Desktop

DChIPRep

Compares profiles of enrichment in histone modifications around classes of…

Compares profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). DChIPRep tests for differential enrichment at each nucleotide…

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PeakAnalyzer
Desktop

PeakAnalyzer

Allows users to process genomic loci with an emphasis on datasets consisting of…

Allows users to process genomic loci with an emphasis on datasets consisting of ChIP-derived signal peaks. PeakAnalyzer is an open source software composed of two main functions: (i) PeakSplitter…

geneXtendeR
Desktop

geneXtendeR

An R/Bioconductor package for histone modification ChIP-seq analysis.…

An R/Bioconductor package for histone modification ChIP-seq analysis. geneXtendeR is designed to optimally annotate a histone modification ChIP-seq peak input file with functionally important genomic…

CATCHprofiles
Desktop

CATCHprofiles Clustering and AlignmenT of ChIp profiles

A standalone for exhaustive pattern detection in ChIP profiling data.…

A standalone for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering…

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Heat*seq
Web
Desktop

Heat*seq

A web-tool that allows genome scale comparison of high throughput experiments…

A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise…

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compEpiTools
Desktop

compEpiTools

Facilitates several typical operations related to the quantification of the…

Facilitates several typical operations related to the quantification of the sequencing signal in a set of genomic regions. compEpiTools provides a number of methods to score these data in regions of…

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COUGER
Desktop
Web
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PTHGRN
Web

PTHGRN Post-Translational Hierarchical Gene Regulatory Network

An open web server to unravel relationships among PTMs, TFs, epigenetic…

An open web server to unravel relationships among PTMs, TFs, epigenetic modifications and gene expression. PTHGRN accepts three input: PPI, ChIP-seq binding peaks of TFs and epigenetic modifications,…

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ePIANNO
Web

ePIANNO ePIgenomics ANNOtation tool

Helps users to explore the associations between protein-binding event,…

Helps users to explore the associations between protein-binding event, disease-associated genomic variants, and information of general populations by annotating the ChIP-seq datasets. ePIANNO is a…

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DGW
Desktop

DGW Dynamic Genome Warping

Enables construction of robust speech recognisers undeterred by the variability…

Enables construction of robust speech recognisers undeterred by the variability in pitch and speed of enunciation. DGW is based on the classical Dynamic Time Warping algorithm. It can align genomic…

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PAPST
Desktop

PAPST Peak Assignment and Profile Search Tool

A user friendly program for analysis of ChIP-Seq experiments. PAPST allows…

A user friendly program for analysis of ChIP-Seq experiments. PAPST allows users to interact with the significant peaks called from ChIP-seq experiments. It allows powerful co-localization analysis…

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ChIPseek
Web

ChIPseek

A web-based tool for ChIP data analysis providing summary statistics in graphs…

A web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses.

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FullSignalRanke…
Desktop

FullSignalRanker

To fully understand a gene's function, it is essential to develop…

To fully understand a gene's function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the combinatorial gene transcription. To this end, we propose…

GeneNetworkBuil…
Desktop

GeneNetworkBuilder

A package for discovering direct or indirect targets of transcription factors…

A package for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential…

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LPCHP
Desktop

LPCHP Linear predictive coding histone profile

Allows the capture and comparison of ChIP-seq histone profiles. LPCHP can be…

Allows the capture and comparison of ChIP-seq histone profiles. LPCHP can be used as an alternative to read intensities, its utility may extend beyond ChIP-seq to other next-generation sequencing…

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Seqinspector
Web

Seqinspector

Facilitates the functional annotation and discovery of transcription factor…

Facilitates the functional annotation and discovery of transcription factor binding sites on promoters of co-expressed transcripts, signals from ChIP-seq experiments and any other set of genomic…

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CASSys
Web

CASSys ChIP-seq data Analysis Software System

An integrated, user-friendly software system, spanning all steps of ChIP-seq…

An integrated, user-friendly software system, spanning all steps of ChIP-seq data analysis. CASSys supersedes the laborious application of several single command line tools. CASSys provides…

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