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

ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChAMP")

 

PDF	R Script	Package
PDF		Reference Manual

Details

biocViews	Bioinformatics, CopyNumberVariants, DNAmethylation, DataImport, DifferentialMethylation, IlluminaChip, Preprocessing, QualityControl, SNP, Software
Version	1.0.7
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
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	ChAMP_1.0.7.tar.gz
Windows Binary	ChAMP_1.0.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ChAMP_1.0.7.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats