Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

ChIP-chip data analysis bioinformatics 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. This…
G T A T C G C T A
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.

G T A T C G C T A
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.

MDscan
Desktop
Web

MDscan Motif Discovery scan

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

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…

CEAS
Desktop
Web

CEAS Cis-regulatory Element Annotation System

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

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…

BAC
Desktop

BAC Bayesian analysis of ChIP-chip

Detects transcription factor bound regions, which incorporate the dependence…

Detects transcription factor bound regions, which incorporate the dependence between probes while making little assumptions about the bound regions (e.g., length). BAC is robust to probe outliers…

G T A T C G C T A
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…

TileMap
Desktop

TileMap

A computational tool to make tiling array analysis and to detect genomic loci…

A computational tool to make tiling array analysis and to detect genomic loci that show hybridization patterns of interest. TileMap includes functions to (i) compute probe-level test-statistics…

ChIPOTle
Desktop

ChIPOTle Chromatin ImmunoPrecipitation On Tiled arrays

Performs peak detection in chromatin immunoprecipitation (ChIP)-chip signal.…

Performs peak detection in chromatin immunoprecipitation (ChIP)-chip signal. ChIPOTle was created for the analysis of ChIP-chip data obtained using tiled arrays, which allow to exploit both the…

Trawler
Desktop

Trawler

An integrated pipeline for the analysis of large scale…

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…

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.…

Ringo
Desktop

Ringo

A package that facilitates the analysis of ChIP-chip experiments by providing…

A package that facilitates the analysis of ChIP-chip experiments by providing functionality for data import, quality assessment, normalization and visualization of the data, and the detection of…

rMAT
Desktop

rMAT

A package that allows the identification of regions enriched for transcription…

A package that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays. rMAT is based on the popular MAT software. It…

ACME
Desktop

ACME Algorithms for Calculating Microarray Enrichment

A package based on a set of tools for analysing tiling array ChIP/chip, DNAse…

A package based on a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". ACME does not…

G T A T C G C T A
rGADEM
Desktop

rGADEM

A package containing an extended version of the original GADEM C code. For…

A package containing an extended version of the original GADEM C code. For ChIP-Seq data, a key improvement is that, on multicore computers, rGADEM can take advantage of multithreading via Grand…

Starr
Desktop

Starr

Facilitates comparative analysis of ChIP-chip data across experiments and…

Facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms. Starr provides functions for data import, quality assessment, data visualization and…

CMARRT
Desktop

CMARRT

Represents an algorithm that can be used with any tiling platform and which…

Represents an algorithm that can be used with any tiling platform and which extends the standard moving average approach commonly used in the analysis of ChIP-chip data by incorporating the…

ChIPmeta
Desktop

ChIPmeta

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

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

G T A T C G C T A
ChIPXpress
Desktop

ChIPXpress

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

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

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…

CoCAS
Desktop

CoCAS ChIP-on-Chip Analysis Suite

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

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

G T A T C G C T A
ChIP-PED
Desktop

ChIP-PED

Predicts biological contexts in which a transcription factor (TF) and its…

Predicts biological contexts in which a transcription factor (TF) and its target genes are functionally active. ChIP-PED is a software which allows users to extend the scope of their ChIPx data to…

Sandcastle
Desktop
Amadeus
Desktop

Amadeus

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

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…

NTAP
Desktop

NTAP NimbleGen Tilingarray Analysis Package

It was developed in the process of our own generated NimbleGen tiling array…

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

G T A T C G C T A
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.

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…

iChip
Desktop

iChip

A package that uses hidden Ising models to identify enriched genomic regions in…

A package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. iCHip can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and…

RankMotif++
Desktop

RankMotif++

Designed for finding motifs whenever sequences are associated with a…

Designed for finding motifs whenever sequences are associated with a semi-quantitative measure of protein-DNA-binding affinity. RankMotif++ algorithm uses the microarray data to infer relative…

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…

G T A T C G C T A
CisFinder
Desktop
Web

CisFinder

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

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…

RAP
Desktop

RAP Rank Align PWM

Infers binding-site motifs from PBM data. RAP outperforms prior art both in…

Infers binding-site motifs from PBM data. RAP outperforms prior art both in predicting in vitro binding and in producing motifs similar to literature motifs. The method works in four phases: (i)…

G T A T C G C T A
HATSEQ
Desktop

HATSEQ Hypergeometric Analysis of Tiling-array and SEQuence data

A powerful tool that accurately identifies functional regions of interest…

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…

GenomeStudio
Desktop

GenomeStudio

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

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…

CoCo
Web

CoCo ChIP-on-Chip online

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

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…

G T A T C G C T A
ChromaSig
Desktop

ChromaSig

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

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…

TAAPP
Web

TAAPP Tiling Array Analysis Pipeline for Prokaryotes

Provides a computational pipeline which is tailored for prokaryotic tiling…

Provides a computational pipeline which is tailored for prokaryotic tiling array data. TAAPP consists of two modules: the first module handles normalized data from single color arrays, identifies…

Related Websites
Information

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