rMAT

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

Bioconductor version: 2.9

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 anf 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 crchuq.ulaval.ca> and Raphael Gottardo <rgottard at fhcrc.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("rMAT")

To cite this package in a publication, start R and enter:

    citation("rMAT")

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