To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ChAMP")

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

ChAMP

 

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: Release (3.1)

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. In addition their is a method to help calculate hmC using BS and oxBS samples.

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

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 is not available
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
Text   NEWS

Details

biocViews CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.6.0
In Bioconductor since BioC 2.13 (R-3.0) (2 years)
License GPL-3
Depends R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, IRanges, GenomicRanges
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Build Report  

Package Archives

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

Package Source ChAMP_1.6.0.tar.gz
Windows Binary ChAMP_1.6.0.zip
Mac OS X 10.6 (Snow Leopard) ChAMP_1.6.0.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

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