Package: RnBeads
Title: RnBeads
Description: RnBeads facilitates comprehensive analysis of various types of DNA
    methylation data at the genome scale.
Authors@R: c(
    person("Yassen", "Assenov", email = "yassen@mpi-inf.mpg.de",
    role = c("aut")),
    person("Pavlo", "Lutsik", email = "p.lutsik@mx.uni-saarland.de",
    role = c("aut")),
    person("Michael", "Scherer", email = "mscherer@mpi-inf.mpg.de",
    role = c("aut")),
    person("Fabian", "Mueller", email = "rnbeads@mpi-inf.mpg.de",
    role = c("aut", "cre")))
Date: 2021-03-01
Version: 2.8.1
Suggests: Category, GOstats, Gviz,
        IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
        RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach,
        doParallel, ggbio, isva, mclust, mgcv, minfi, nlme,
        org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog,
        rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue,
        argparse, glmnet, GLAD,
        IlluminaHumanMethylation450kanno.ilmn12.hg19, scales,
        missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit,
        MethylSeekR
Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
        GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2),
        gplots, gridExtra, limma, matrixStats, methods, illuminaio,
        methylumi, plyr
Imports: IRanges
License: GPL-3
biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
        QualityControl, Preprocessing, BatchEffect,
        DifferentialMethylation, Sequencing, CpGIsland, ImmunoOncology,
        TwoChannel, DataImport
Collate: 'CNV.R' 'Report-class.R' 'Report-methods.R'
        'ReportPlot-class.R' 'ReportPlot-methods.R'
        'RnBDiffMeth-class.R' 'bigFf.R' 'RnBSet-class.R'
        'RnBeadSet-class.R' 'RnBeadRawSet-class.R' 'RnBeads-package.R'
        'RnBiseqSet-class.R' 'agePrediction.R' 'annotations.R'
        'batch.R' 'batch.quality.R' 'bmiq.R' 'cellTypeAdjustment.R'
        'clusterArchitecture.R' 'clusterArchitectureSGE.R'
        'clusterArchitectureSLURM.R' 'clustering.R' 'combining.R'
        'computeCluster.R' 'controlPlots.R' 'controlPlotsBiSeq.R'
        'dataExport.R' 'dataImport.R' 'differentialMethylation.R'
        'differentialVariability.R' 'enmix.R' 'enrichment.R'
        'exportGEO.R' 'filtering.R' 'filteringSummary.R' 'genomewide.R'
        'greedycut.R' 'immune.R' 'loading.R' 'logger.R' 'lolaUtils.R'
        'main.R' 'normalization.R' 'options.R' 'parallelProcessing.R'
        'plottingUtils.R' 'profiles.R' 'qualityControl.R' 'readGEO.R'
        'regionDescription.R' 'regionProfiles.R' 'segmentation.R'
        'sex.R' 'subSegments.R' 'sva.R' 'utilities.R' 'wbcInference.R'
RoxygenNote: 7.1.0
git_url: https://git.bioconductor.org/packages/RnBeads
git_branch: RELEASE_3_12
git_last_commit: b87f536
git_last_commit_date: 2021-03-01
Date/Publication: 2021-03-01
NeedsCompilation: no
Packaged: 2021-03-02 03:01:34 UTC; biocbuild
Author: Yassen Assenov [aut],
  Pavlo Lutsik [aut],
  Michael Scherer [aut],
  Fabian Mueller [aut, cre]
Maintainer: Fabian Mueller <rnbeads@mpi-inf.mpg.de>
Built: R 4.0.3; ; 2021-04-03 21:36:27 UTC; unix
