ChAMP

DOI: 10.18129/B9.bioc.ChAMP    

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Release (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>

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	2.9.10
In Bioconductor since	BioC 2.13 (R-3.0) (4.5 years)
License	GPL-3
Depends	R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest
Imports	prettydoc, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
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.

Source Package	ChAMP_2.9.10.tar.gz
Windows Binary	ChAMP_2.9.10.zip
Mac OS X 10.11 (El Capitan)	ChAMP_2.9.10.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChAMP
Package Short Url	http://bioconductor.org/packages/ChAMP/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive