:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
ChIPmeta is a software for the joint analysis of ChIP-seq and ChIP-chip data. Individual channel-level analysis and joint analysis are performed using hidden Markov models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
H. Choi, A.I. Nesvizhskii, D. Ghosh, and Z.S. Qin (2009),
Hierarchical HMM with Application to Joint Analysis of ChIP-seq and ChIP-chip Data.
Bioinformatics, 25, 1715-21.
:: DESCRIPTION
TiMAT is an open-source, Java based set of scripts used for processing chip-chip tiling array experiments. Its four main functionalities are (1) smooth noisy signals, (2) optionally calculate false discovery rates, (3) identify enriched intervals and (4) identify peaks within these enriched intervals. While parts of TiMAT might be used in analyzing expression arrays, other parts, such as the symmetric null-p calculations are not appropriate for such experiments– TiMAT is designed for chip-chip experiments.
::DEVELOPER
the Berkeley Drosophila Transcription Network Project,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
