ChAMP

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Development (3.24)

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")):

Yuan Tian. ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC. doi:10.18129/B9.bioc.ChAMP, R package version 2.43.1, https://bioconductor.org/packages/ChAMP.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version	2.43.1
In Bioconductor since	BioC 2.13 (R-3.0) (13 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, ggplot2, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
System Requirements
URL

Suggests	knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	GeoTcgaData
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ChAMP_2.43.1.tar.gz
Windows Binary (x86_64)	ChAMP_2.43.1.zip
macOS Binary (big-sur-x86_64)	ChAMP_2.43.1.tgz
macOS Binary (sonoma-arm64)	ChAMP_2.43.1.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	https://bioconductor.org/packages/ChAMP/
Package Downloads Report	Download Stats