To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ChAMP")

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

ChAMP

 

   

This is the development version of ChAMP; for the stable release version, see ChAMP.

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Development (3.6)

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("http://bioc.ism.ac.jp/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 2.9.3
In Bioconductor since BioC 2.13 (R-3.0) (3.5 years)
License GPL-3
Depends R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest
Imports sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), 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_2.9.3.tar.gz
Windows Binary ChAMP_2.9.3.zip
Mac OS X 10.11 (El Capitan) ChAMP_2.9.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChAMP
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

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