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Bioconductor - ChAMP

ChAMP

This is the released version of ChAMP; for the devel version, see ChAMP.

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel Version 2.38.0 In Bioconductor since BioC 2.13 (R-3.0) (11.5 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 System Requirements URL See More Package Archives

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

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