To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChAMP")

In most cases, you don't need to download the package archive at all.

ChAMP

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see ChAMP.

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: 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 <champ450k at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.4.1
In Bioconductor since BioC 2.13 (R-3.0) (2.5 years)
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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Depends On Me
Imports Me
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Build Report

Package Archives

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

Package Source ChAMP_1.4.1.tar.gz
Windows Binary ChAMP_1.4.1.zip
Mac OS X 10.6 (Snow Leopard) ChAMP_1.4.1.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.4.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.0
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

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