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

Bioconductor version: Release (3.1)

This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!

Author: Charles Cheung and Arnaud Droit and Raphael Gottardo

Maintainer: Arnaud Droit <arnaud.droit at> and Raphael Gottardo <rgottard at>

Citation (from within R, enter citation("rMAT")):


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PDF R Script The rMAT users guide
PDF   Reference Manual


biocViews Microarray, Preprocessing, Software
Version 3.18.0
In Bioconductor since BioC 2.4 (R-2.9) (6.5 years)
License Artistic-2.0
Depends R (>= 2.9.0), BiocGenerics(>= 0.1.3), IRanges(>= 1.13.10), Biobase(>= 2.15.1), affxparser
Imports stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4
Suggests GenomeGraphs, rtracklayer
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Imports Me
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