Package: ChAMP
Type: Package
Title: Chip Analysis Methylation Pipeline for Illumina
        HumanMethylation450 and EPIC
Version: 2.40.0
Date: 2020-11-2
Description: 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.
Authors@R: c(person("Tian","Yuan", role = c("cre", "aut"),
                    email = "champ450k@gmail.com"),
		person("Tiffany","Morris",role = "ctb"),
             person("Lee", "Stirling", role = "ctb"),
             person("Andrew", "Feber", role = "ctb"),
	     person("Andrew", "Teschendorff", role = "ctb"),
	     person("Ankur", "Chakravarthy", role = "ctb"))
License: GPL-3
VignetteBuilder: knitr
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
biocViews: Microarray, MethylationArray, Normalization, TwoChannel,
        CopyNumber, DNAMethylation
Suggests: knitr,rmarkdown
Author: Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb],
        Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur
        Chakravarthy [ctb]
Maintainer: Yuan Tian <champ450k@gmail.com>
NeedsCompilation: no
Packaged: 2025-11-11 20:20:28 UTC; root
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:17:05 UTC
RemoteUrl: https://github.com/bioc/ChAMP
RemoteRef: RELEASE_3_22
RemoteSha: fa068cf19bfa4d501e6e17ce656cdc950c10d210
Built: R 4.5.2; ; 2025-11-12 03:39:43 UTC; windows
