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

 

   

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Release (3.4)

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

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

Maintainer: Yuan Tian <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

HTML R Script ChAMP: The Chip Analysis Methylation Pipeline
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 2.4.0
In Bioconductor since BioC 2.13 (R-3.0) (3 years)
License GPL-3
Depends R (>= 3.3), minfi, ChAMPdata(>= 2.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest
Imports sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly, RColorBrewer, dendextend, matrixStats
LinkingTo
Suggests knitr, rmarkdown
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_2.4.0.tar.gz
Windows Binary ChAMP_2.4.0.zip
Mac OS X 10.9 (Mavericks) ChAMP_2.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.4
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: