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 = "assenov@gmail.com",
    role = c("aut")),
    person("Christoph", "Bock", email = "cbock@cemm.at",
    role = c("aut")),
    person("Pavlo", "Lutsik", email = "p.lutsik@dkfz.de",
    role = c("aut")),
    person("Michael", "Scherer", email = "mscherer@mpi-inf.mpg.de",
    role = c("aut")),
    person("Fabian", "Mueller", email = "team@rnbeads.org",
    role = c("aut", "cre")))
Date: 2024-04-22
Version: 2.25.0
Suggests:
    Category,
    GOstats,
    Gviz,
    IlluminaHumanMethylation450kmanifest,
    RPMM,
    RnBeads.hg19,
    RnBeads.mm9,
    RnBeads.hg38,
    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,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    scales,
    missMethyl,
    impute,
    shiny,
    shinyjs,
    plotrix,
    hexbin,
    RUnit,
    MethylSeekR,
    sesame
Depends:
    R (>= 3.0.0),
    BiocGenerics,
    S4Vectors (>= 0.9.25),
    GenomicRanges,
    MASS,
    cluster,
    ff,
    fields,
    ggplot2 (>= 0.9.2),
    gplots,
    grid,
    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'
    'clusterArchitectureLSF.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'
    'normalizationMethods.R'
    'options.R'
    'parallelProcessing.R'
    'plottingUtils.R'
    'profiles.R'
    'qualityControl.R'
    'readGEO.R'
    'regionDescription.R'
    'regionProfiles.R'
    'segmentation.R'
    'sesame.R'
    'sex.R'
    'subSegments.R'
    'sva.R'
    'utilities.R'
    'wbcInference.R'
RoxygenNote: 7.3.1