ChAMP

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ChAMP.

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel

Version 2.28.0

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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Suggests knitr, rmarkdown

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Package Archives

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

Source Package ChAMP_2.28.0.tar.gz

Windows Binary ChAMP_2.28.0.zip

macOS Binary (x86_64) ChAMP_2.28.0.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

Old Source Packages for BioC 3.16 Source Archive