ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: Development (3.0)

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

Author: Tiffany Morris [cre, aut], Lee Butcher [aut], Andrew Feber [aut], Andrew Teschendorff [aut], Ankur Chakravarthy [aut]

Maintainer: Tiffany Morris <tiffany.morris at ucl.ac.edu>

To install this package, start R and enter:

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

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

Documentation

PDF R Script Package
PDF   Reference Manual

Details

biocViews CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.3.12
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-3
Depends R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr
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Package Downloads

Package Source ChAMP_1.3.12.tar.gz
Windows Binary ChAMP_1.3.12.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChAMP_1.3.12.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.3.12.tgz
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