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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 (3.19)

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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ChAMP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("ChAMP")
ChAMP: The Chip Analysis Methylation Pipeline HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 2.33.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest, DT, RPMM
Imports prettydoc, Hmisc, globaltest, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, kpmt, ggplot2, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
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Package Archives

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

Source Package ChAMP_2.33.0.tar.gz
Windows Binary ChAMP_2.33.0.zip
macOS Binary (x86_64) ChAMP_2.33.0.tgz
macOS Binary (arm64) ChAMP_2.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChAMP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChAMP
Bioc Package Browser https://code.bioconductor.org/browse/ChAMP/
Package Short Url https://bioconductor.org/packages/ChAMP/
Package Downloads Report Download Stats