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

Algorithms for Calculating Microarray Enrichment
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

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...

BAC

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

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.

CisFinder

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...

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

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

CoCo

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

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.

MDscan

Motif Discovery scan
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...

NTAP

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

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

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.

Trawler

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...