minfi

Package: minfi
Version: 1.18.2
Title: Analyze Illumina's methylation arrays
Description: Tools for analyzing and visualizing Illumina's methylation array data.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
email = "kasperdanielhansen@gmail.com"),
person("Martin", "Aryee", role = "aut"),
person(c("Rafael", "A."), "Irizarry", role = "aut"),
person(c("Andrew", "E."), "Jaffe", role = "ctb"),
person("Jovana", "Maksimovic", role = "ctb"),
person(c("E.", "Andres"), "Houseman", role = "ctb"),
person("Jean-Philippe", "Fortin", role = "ctb"),
person("Tim", "Triche", role = "ctb"),
person(c("Shan", "V."), "Andrews", role = "ctb"))
Depends: methods, BiocGenerics (>= 0.15.3), Biobase (>= 2.17.8),
lattice, GenomicRanges, SummarizedExperiment (>= 1.1.6),
Biostrings, bumphunter (>= 1.1.9)
Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
minfiData (>= 0.4.1), FlowSorted.Blood.450k (>= 1.0.1), RUnit,
digest, BiocStyle, knitr, rmarkdown
Imports: S4Vectors, GenomeInfoDb, IRanges, beanplot, RColorBrewer,
nor1mix, siggenes, limma, preprocessCore, illuminaio,
matrixStats (>= 0.50.0), mclust, genefilter, nlme, reshape,
MASS, quadprog, data.table, GEOquery, stats, grDevices,
graphics, utils
Collate: generics.R mset.R rset.R rgset.R gmset.R grset.R utils.R
manifest.R anno.R minfiQC.R getSex.R dmr.R blocks.R plot.R
plotBetasByType.R preprocess.R preprocessSwan.R
preprocessQuantile.R preprocessNoob.R preprocessFunnorm.R qc.R
read.450k.R read.meth.R read.geo.R read.manifest.R bumphunter.R
estimateCellCounts.R gaphunter.R compartments.R
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/kasperdanielhansen/minfi
BugReports: https://github.com/kasperdanielhansen/minfi/issues
LazyData: yes
biocViews: DNAMethylation, Microarray, TwoChannel, DataImport,
Preprocessing, QualityControl
NeedsCompilation: no
Packaged: 2016-05-16 03:05:11 UTC; biocbuild
Author: Kasper Daniel Hansen [cre, aut],
Martin Aryee [aut],
Rafael A. Irizarry [aut],
Andrew E. Jaffe [ctb],
Jovana Maksimovic [ctb],
E. Andres Houseman [ctb],
Jean-Philippe Fortin [ctb],
Tim Triche [ctb],
Shan V. Andrews [ctb]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'minfi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'minfi'
    finding HTML links ... done
    GenomicMethylSet-class                  html  
Rd warning: /tmp/RtmpIotP8o/R.INSTALL77ec6c71054f/minfi/man/GenomicMethylSet-class.Rd:115: missing file link 'RangedSummarizedExperiment'
    GenomicRatioSet-class                   html  
Rd warning: /tmp/RtmpIotP8o/R.INSTALL77ec6c71054f/minfi/man/GenomicRatioSet-class.Rd:105: missing file link 'RangedSummarizedExperiment'
    IlluminaMethylationAnnotation-class     html  
    IlluminaMethylationManifest-class       html  
    MethylSet-class                         html  
    finding level-2 HTML links ... done

    RGChannelSet-class                      html  
    RatioSet-class                          html  
    blockFinder                             html  
    bumphunter                              html  
    compartments                            html  
    controlStripPlot                        html  
    cpgCollapse                             html  
    densityBeanPlot                         html  
    densityPlot                             html  
    detectionP                              html  
    dmpFinder                               html  
    estimateCellCounts                      html  
    fixMethOutliers                         html  
    gaphunter                               html  
    getAnnotation                           html  
    getGenomicRatioSetFromGEO               html  
    getQC                                   html  
    getSex                                  html  
    logit2                                  html  
    makeGenomicRatioSetFromMatrix           html  
    mapToGenome-methods                     html  
    mdsPlot                                 html  
    minfi-deprecated                        html  
    minfi-package                           html  
    minfiQC                                 html  
    plotBetasByType                         html  
    plotCpg                                 html  
    preprocessFunnorm                       html  
    preprocessIllumina                      html  
    preprocessNoob                          html  
    preprocessQuantile                      html  
    preprocessRaw                           html  
    preprocessSwan                          html  
    qcReport                                html  
    ratioConvert-methods                    html  
    read.450k                               html  
    read.450k.exp                           html  
    read.450k.sheet                         html  
    read.metharray                          html  
    read.metharray.exp                      html  
    read.metharray.sheet                    html  
    readGEORawFile                          html  
    readTCGA                                html  
    utils                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (minfi)
Making 'packages.html' ... done