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