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, Lee Butcher, Andy Feber, Andrew Teschendorff, Ankur Chakravarthy and Stephan Beck

Maintainer: Tiffany Morris <Tiffany.Morris at ucl.ac.uk>

To install this package, start R and enter:

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

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

    citation("ChAMP")

Documentation

PDF R Script Package
PDF   Reference Manual

Details

biocViews Bioinformatics, CopyNumberVariants, DNAMethylation, DataImport, DifferentialMethylation, IlluminaChip, Preprocessing, QualityControl, SNP, Software
Version 1.3.0
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
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Package Downloads

Package Source ChAMP_1.3.0.tar.gz
Windows Binary ChAMP_1.3.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChAMP_1.3.0.tgz
Mac OS X 10.9 (Mavericks)
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