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 3.2 of Bioconductor; for the stable, up-to-date release version, see ChAMP.

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: 3.2

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:// 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 Package
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.8.2
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, IRanges, GenomicRanges
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source ChAMP_1.8.2.tar.gz
Windows Binary ChAMP_1.8.2.zip
Mac OS X 10.6 (Snow Leopard) ChAMP_1.8.0.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.8.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.2
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

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