ChAMP

DOI: 10.18129/B9.bioc.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 (3.8)

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:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ChAMP", version = "devel")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChAMP")

 

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

Details

biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 2.11.5
In Bioconductor since BioC 2.13 (R-3.0) (5 years)
License GPL-3
Depends R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest
Imports prettydoc, Hmisc, globaltest, 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
Links To Me
Build Report  

Package Archives

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

Source Package ChAMP_2.11.5.tar.gz
Windows Binary ChAMP_2.11.5.zip
Mac OS X 10.11 (El Capitan) ChAMP_2.11.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChAMP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChAMP
Package Short Url http://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats

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