This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

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

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 (3.18)

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 "4.3") 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

Reference Manual PDF

Details

biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 2.31.0
In Bioconductor since BioC 2.13 (R-3.0) (10 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
Linking To
Suggests knitr, rmarkdown
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me GeoTcgaData
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary ChAMP_2.31.0.zip
macOS Binary (x86_64) ChAMP_2.31.0.tgz
macOS Binary (arm64)
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