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.
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kmerHMM

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

CEAS

Integrates many useful tools to simplify ChIP-chip analysis for biologists.


ACME

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

Adriaens et al., 2012, BMC genomics

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies.

BAC

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

CATCHprofiles

A tool for exploring patterns in ChIP profiling data.

ChIPmeta

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

ChIPOTle

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

ChIPpeakAnno

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

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

ChIPXpress

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

CisGenome

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

Cistrome

Galaxy-based web service for analysis of ChIP data.

CoCAS

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

CoCo

A computational tool that allows the user to search, visualise and store different data associated with gene expression.

GeneNetworkBuilder

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

GenomeStudio

Visualize and analyze data generated by all of Illumina's platforms.

iChip

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

les

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

NTAP

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

Ringo

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

rMAT

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

Starr

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

TileMap

A software tool for ChIP-chip peak calling.

Zheng et al., 2007, Biometrics

ChIP-chip: data, model, and analysis.