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ChIP-on-chip software tools

Microarray software tools

Protein-DNA interactions are involved in many essential biological processes such as transcription, splicing, replication and DNA repair. ChIP-on-chip is a technique that combines chromatin immunoprecipitation with microarray technology (Oberley et al., 2004). This technique is well suited for a comprehensive analysis of transcription factor binding sites, histone modification patterns, and nucleosome occupancy.

Algorithms for Calculating Microarray Enrichment

OMIC_01976

Algorithms for Calculating Microarray Enrichment
ACME

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other…

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment".

Amadeus

OMIC_06286

Amadeus

A user-friendly software platform for genome-scale detection of known and novel motifs…

A user-friendly software platform for genome-scale detection of known and novel motifs (recurring patterns) in DNA sequences, applicable to a wide range of motif discovery tasks. Amadeus outperforms extant tools and sets a new standard for motif…

BAC

OMIC_00801

BAC

This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip…

This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

CATCHprofiles

OMIC_02171

CATCHprofiles

A tool for exploring patterns in ChIP profiling data.

A tool for exploring patterns in ChIP profiling data.

ChIP-on-Chip Analysis Suite

OMIC_02583

ChIP-on-Chip Analysis Suite
CoCAS

A standalone software suite which implements optimized ChIP-on-chip data normalization,…

A standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports.

ChIP-on-Chip online

OMIC_00805

ChIP-on-Chip online
CoCo

A web-based tool dedicated to ChIP-on-chip data visualization, analysis and knowledge…

A web-based tool dedicated to ChIP-on-chip data visualization, analysis and knowledge storage. To support target gene assignment, CoCo integrates diverse types of meta-data, including the genomic context around the transcription factor (TF)-bound…

ChIPmeta

OMIC_02172

ChIPmeta

Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

ChIPOTle

OMIC_00803

ChIPOTle

A peak-finding algorithm used to analyze ChIP-chip microarray data.

A peak-finding algorithm used to analyze ChIP-chip microarray data.

ChIPpeakAnno

OMIC_00804

ChIPpeakAnno

The package includes functions to retrieve the sequences around the peak, obtain enriched…

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

ChIPseek

OMIC_04869

ChIPseek

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

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

ChIPXpress

OMIC_00516

ChIPXpress

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly…

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data.

ChromaSig

OMIC_09487

ChromaSig

An unsupervised learning method to find, in an unbiased fashion, commonly occurring…

An unsupervised learning method to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. ChromaSig recovers known patterns associated with transcriptional enhancers and promoters.

Cis-regulatory Element Annotation System

OMIC_00802

Cis-regulatory Element Annotation System
CEAS

A software tool designed to characterize genome-wide protein-DNA interaction patterns…

A software tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. CEAS provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene…

CisFinder

OMIC_06290

CisFinder

A tool for finding over-representing short DNA motifs (e.g., transcription factor binding…

A tool for finding over-representing short DNA motifs (e.g., transcription factor binding motifs) and estimates the Position Frequency Matrix (PFM) directly from word counts. It is designed for the analysis of ChIP-chip and ChIP-seq data and can…

CisGenome

OMIC_00423

CisGenome

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

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

Cistrome

OMIC_02173

Cistrome

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

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 categories, from preliminary peak calling and…

GeneNetworkBuilder

OMIC_01971

GeneNetworkBuilder

Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data.

Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data.

GenomeStudio

OMIC_00854

GenomeStudio

Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports…

Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports the primary analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into…

Hypergeometric Analysis of Tiling-array and…

OMIC_09313

Hypergeometric Analysis of Tiling-array and SEQuence data
HATSEQ

A powerful tool that accurately identifies functional regions of interest (ROIs) on the…

A powerful tool that accurately identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. HATSEQ also includes a number of built-in post-analyses with which…

iChip

OMIC_00807

iChip

This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip…

This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.

kmerHMM

OMIC_02662

kmerHMM

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and…

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation.

les

OMIC_02045

les

Estimates Loci of Enhanced Significance (LES) in tiling microarray data.

Estimates Loci of Enhanced Significance (LES) in tiling microarray data.

Motif Discovery scan

OMIC_06288

Motif Discovery scan
MDscan

A computational method that examines the ChIP-array-selected sequences and searches for…

A computational method that examines the ChIP-array-selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. MDscan combines the advantages of two widely adopted motif search strategies, word…

NimbleGen Tilingarray Analysis Package

OMIC_00808

NimbleGen Tilingarray Analysis Package
NTAP

It was developed in the process of our own generated NimbleGen tiling array data analysis.

It was developed in the process of our own generated NimbleGen tiling array data analysis.

rGADEM

OMIC_00491

rGADEM

An efficient de novo motif discovery tool for large-scale genomic sequence data. rGADEM…

An efficient de novo motif discovery tool for large-scale genomic sequence data. rGADEM provides a complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data.

Ringo

OMIC_00809

Ringo

This package facilitates the primary analysis of ChIP-chip data.

This package facilitates the primary analysis of ChIP-chip data.

rMAT

OMIC_00810

rMAT

R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip…

R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.

Software for the Analysis and Normalisation of…

OMIC_11939

Software for the Analysis and Normalisation of Data from ChIP-chip AssayS…
Sandcastle

An R package which allows for comparative analyses of data from multiple experiments by…

An R package which allows for comparative analyses of data from multiple experiments by normalizing all datasets to a common background. Sandcastle contains a new normalisation procedure, enabling the extraction of previously irretrievable…

Starr

OMIC_00811

Starr

Facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling…

Facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays.

TileMap

OMIC_00812

TileMap

A software tool for ChIP-chip peak calling.

A software tool for ChIP-chip peak calling.

Trawler

OMIC_06287

Trawler

An integrated pipeline for the analysis of large scale chromatin-immunoprecipitation…

An integrated pipeline for the analysis of large scale chromatin-immunoprecipitation (ChIP) data. From the immunoprecipitated sequences, the over-represented motifs are extracted and clustered into position weight matrices (PWMs). The…

W-ChIPeaks

OMIC_07422

W-ChIPeaks

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

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 previously published experimental data.

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