ReMoDiscovery – Inferring Transcriptional Module networks from ChIP-chip-, motif- and microarray data

ReMoDiscovery

:: DESCRIPTION

ReMoDiscovery is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles.

::DEVELOPER

Kathleen Marchal 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 ReMoDiscovery

:: MORE INFORMATION

Citation

Genome Biol. 2006;7(5):R37. Epub 2006 May 5.
Inferring transcriptional modules from ChIP-chip, motif and microarray data.
Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K.

MAT build 3 – Model-based Analysis of Tiling-arrays for ChIP-chip

MAT build 3

:: DESCRIPTION

MAT (Model-based Analysis of Tiling-array) detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MAT

:: MORE INFORMATION

Citation:

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M and Liu XS:
Model-based analysis of tiling-arrays for ChIP-chip.
Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462.

MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

W-ChIPeaks – Process ChIP-chip and ChIP-seq data

W-ChIPeaks

:: DESCRIPTION

W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.

Starr 1.24.0 – Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Starr 1.24.0

:: DESCRIPTION

Starr is open-source R/Bioconductor package that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms.

::DEVELOPER

Tresch Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Starr

:: MORE INFORMATION

Citation

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
Zacher B, Kuan PF, Tresch A.
BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194.

ChIPpeakAnno 3.2.1 – Annotate ChIP-seq and ChIP-chip data

ChIPpeakAnno 3.2.1

:: DESCRIPTION

ChIPpeakAnno is a Bioconductor package within the statistical programming environment R 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 genomic regions.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

  ChIPpeakAnno

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237.
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

Ringo 1.33.0 – Analysis of ChIP-chip data

Ringo 1.33.0

:: DESCRIPTION

Ringo is an R 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 ChIP-enriched genomic regions.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

   Ringo

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jun 26;8:221.
Ringo–an R/Bioconductor package for analyzing ChIP-chip readouts.
Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W.

ChIPOTle 2.0 – Tool For The Analysis Of ChIP-chip Data

ChIPOTle 2.0

:: DESCRIPTION

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) is a Microsoft Excel add-in Macro that analyzes yeast ChIP-chip data generated on whole-genome tiled arrays.

::DEVELOPER

Buck Lab

:: SCREENSHOTS

ChIPOTle

:: REQUIREMENTS

  • Windows
  • Excel / Perl

:: DOWNLOAD

 ChIPOTle

:: MORE INFORMATION

Citation

Genome Biol. 2005;6(11):R97.
ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.
Buck MJ, Nobel AB, Lieb JD.

CMARRT 1.3 – Analysis of ChIP-Chip data from Tiling Arrays

CMARRT 1.3

:: DESCRIPTION

CMARRT (Correlation, Moving Average, Robust and Rapid method on Tiling array) is an R package for the analysis of tiling array data that incorporates the correlation structures among probe measurements.

::DEVELOPER

Pei Fen Kuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CMARRT

:: MORE INFORMATION

Citation

Kuan, P., Chun, H., and Keles, S. (2008).
CMARRT: A tool for the analysis of ChIP-Chip data from tiling arrays by incorporating the correlation structure.
Pac Symposium of Biocomputing, 515-526.

Mixer 1.03 – ChIP-chip Analysis by Mixture Model approach

Mixer 1.03

:: DESCRIPTION

Mixer is a mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data. It includes statistical methods for both data normalization and peak detection. The peak detection and quantification relies on a mixer model approach that dissects the distribution of background signals and the Immunoprecipitated signals. In contrast to many existing methods, mixer is more flexible by imposing less restrictive assumptions and allowing a relatively large proportion of peak regions. Robust performance on data sets predicted to contain numerous peaks is very important for the studies of the transcription factors with abundant binding sites, and common chromatin features or epigenetic marks.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  Mixer

:: MORE INFORMATION

Citation

Wei Sun, Michael J Buck, Mukund Patel and Ian J Davis (2009),
Improved ChIP-chip analysis by mixture model approach.
BMC Bioinformatics 2009, 10:173