charm

Package: charm
Type: Package
Title: Analysis of DNA methylation data from CHARM microarrays
Version: 2.18.0
Date: 2016-03-28
Author: Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Maintainer: Peter Murakami <pmurakam@jhu.edu>
Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter
Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses (>=
1.17.39), ff, preprocessCore, methods, stats, Biostrings,
IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils,
limma, parallel, sva (>= 3.1.2)
Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor
Description: This package implements analysis tools for DNA methylation
data generated using Nimblegen microarrays and the McrBC
protocol. It finds differentially methylated regions between
samples, calculates percentage methylation estimates and
includes array quality assessment tools.
License: LGPL (>= 2)
LazyLoad: yes
biocViews: Microarray, DNAMethylation
NeedsCompilation: no
Packaged: 2016-05-04 03:39:37 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'charm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'charm'
    finding HTML links ... done
    bgAdjust                                html  
    clusterMaker                            html  
    cmdsplot                                html  
    controlQC                               html  
    countGC                                 html  
    cpgdensity                              html  
    dmrFdr                                  html  
    dmrFind                                 html  
    dmrFinder                               html  
    dmrPlot                                 html  
    getControlIndex                         html  
    maxDensity                              html  
    methPercent                             html  
    methp                                   html  
    normalizeBetweenSamples                 html  
    normalizeWithinSamples                  html  
    plotDMRs                                html  
    plotDensity                             html  
    plotRegions                             html  
    pmQuality                               html  
    qcReport                                html  
    qval                                    html  
    readCharm                               html  
    regionMatch                             html  
    regionPlot                              html  
    spatialAdjust                           html  
    validatePd                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (charm)
Making 'packages.html' ... done