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.
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…
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.
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.
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
A peak-finding algorithm used to analyze ChIP-chip microarray data.
A peak-finding algorithm used to analyze ChIP-chip microarray data.
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…
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…
ChIPpeakAnno
A package to facilitate batch annotation of enriched peaks identified from…
A package to facilitate 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…
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…
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…
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…
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…
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.
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.
Sandcastle Software for the Analysis and Normalisation of Data from ChIP-chip AssayS of Two or more Linked Experiments
An R package which allows for comparative analyses of data from multiple…
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…
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…
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…
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.
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)…
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…
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…
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…
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…
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…
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…
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…
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…
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.
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…
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.
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…
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…
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…
obsolete
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…
