DOI: 10.18129/B9.bioc.rMAT    

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

Bioconductor version: Release (3.6)

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

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PDF R Script The rMAT users guide
PDF   Reference Manual


biocViews Microarray, Preprocessing, Software
Version 3.28.0
In Bioconductor since BioC 2.4 (R-2.9) (9 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
SystemRequirements GSL (GNU Scientific Library)
URL http://www.rglab.org
Depends On Me
Imports Me
Suggests Me
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Source Package rMAT_3.28.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) rMAT_3.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rMAT
Package Short Url http://bioconductor.org/packages/rMAT/
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