ChAMP

Package: ChAMP
Type: Package
Title: Chip Analysis Methylation Pipeline for Illumina
HumanMethylation450 and EPIC
Version: 1.10.0
Date: 2016-04-25
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. In addition there is a method to help calculate hmC using BS and oxBS samples.
Authors@R: c(person("Tiffany", "Morris", role = c("cre", "aut"),
email = "champ450k@gmail.com"),
person("Tian","Yuan",role = "aut"),
person("Lee", "Stirling", role = "ctb"),
person("Andrew", "Feber", role = "ctb"),
person("Andrew", "Teschendorff", role = "ctb"),
person("Ankur", "Chakravarthy", role = "ctb"))
License: GPL-3
Depends: R (>= 3.2), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports: sva, IlluminaHumanMethylation450kmanifest, limma, RPMM,
DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr,
GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog
biocViews: Microarray, MethylationArray, Normalization, TwoChannel,
CopyNumber, DNAMethylation
Author: Tiffany Morris [cre, aut],
Yuan Tian [aut],
Lee Stirling [ctb],
Andrew Feber [ctb],
Andrew Teschendorff [ctb],
Ankur Chakravarthy [ctb]
Maintainer: Yuan Tian, Tiffany Morris <champ450k@gmail.com>
NeedsCompilation: no
Packaged: 2016-05-04 05:15:29 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ChAMP' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ChAMP'
    finding HTML links ... done
    ChAMP-package                           html  
    champ.CNA                               html  
    champ.DMR                               html  
    champ.MVP                               html  
    champ.SVD                               html  
    champ.TrueMethyl                        html  
    champ.load                              html  
    champ.norm                              html  
    champ.process                           html  
    champ.refbase                           html  
    champ.reffree                           html  
    champ.runCombat                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChAMP)
Making 'packages.html' ... done