ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC


Bioconductor version: Release (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")

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 2.34.0
In Bioconductor since BioC 2.13 (R-3.0) (11 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
System Requirements
URL
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me GeoTcgaData
Links To Me
Build Report Build Report

Package Archives

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

Source Package ChAMP_2.34.0.tar.gz
Windows Binary (x86_64) ChAMP_2.34.0.zip
macOS Binary (x86_64) ChAMP_2.34.0.tgz
macOS Binary (arm64) ChAMP_2.34.0.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