add package

RnBeads


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RnBeads@102199 bc3139a8-67e5-0310-9ffc-ced21a209358

BinaryFiles

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+inst/bin/linux_x86.64/bedGraphToBigWig
+inst/bin/linux_x86.64/bedToBigBed
+inst/bin/macOSX.i386/bedGraphToBigWig
+inst/bin/macOSX.i386/bedToBigBed

DESCRIPTION

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+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 =
+        "[email protected]", role = c("aut")), person("Pavlo",
+        "Lutsik", email = "[email protected]", role =
+        c("aut")), person("Fabian", "Mueller", email =
+        "[email protected]", role = c("aut", "cre")))
+Date: 2015-03-07
+Version: 0.99.22
+Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10,
+        BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn5,
+        Category, GEOquery, GOstats, Gviz,
+        IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
+        RnBeads.hg19, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, 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, sva, wateRmelon, wordcloud, argparse
+Depends: R (>= 3.0.0), BiocGenerics, GenomicRanges, MASS, RColorBrewer,
+        cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra,
+        limma, matrixStats, methods, illuminaio, methylumi, plyr
+Imports: BiocGenerics, IRanges
+License: GPL-3
+biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
+        QualityControl, Preprocessing, BatchEffect,
+        DifferentialMethylation
+Collate: 'CNV.R' 'Report-class.R' 'Report-methods.R'
+        'ReportPlot-class.R' 'ReportPlot-methods.R'
+        'RnBDiffMeth-class.R' 'RnBSet-class.R' 'RnBeadSet-class.R'
+        'RnBeadRawSet-class.R' 'RnBeads-package.R' 'RnBiseqSet-class.R'
+        'annotations.R' 'batch.R' 'batch.quality.R' 'bmiq.R'
+        'cellTypeAdjustment.R' 'clusterArchitecture.R'
+        'clusterArchitectureSGE.R' 'clustering.R' 'computeCluster.R'
+        'controlPlots.R' 'controlPlotsBiSeq.R' 'dataExport.R'
+        'dataImport.R' 'differentialMethylation.R' 'enrichment.R'
+        'filtering.R' 'filteringSummary.R' 'gender.R' 'greedycut.R'
+        'loading.R' 'logger.R' 'main.R' 'normalization.R' 'options.R'
+        'parallelProcessing.R' 'plottingUtils.R' 'profiles.R'
+        'qualityControl.R' 'readGEO.R' 'regionDescription.R'
+        'regionProfiles.R' 'subSegments.R' 'sva.R' 'utilities.R'
+        'wbcInference.R'
+NeedsCompilation: no
+Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut,
+        cre]
+Maintainer: Fabian Mueller <[email protected]>

NAMESPACE

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+# Generated by roxygen2 (4.1.0): do not edit by hand
+
+export(BMIQ)
+export(RnBeadRawSet)
+export(RnBeadSet)
+export(RnBiseqSet)
+export(addRegionSubsegments)
+export(combineTestPvalsMeth)
+export(computeDiffTab.default.region)
+export(computeDiffTab.default.site)
+export(computeDiffTab.extended.site)
+export(create.densityScatter)
+export(create.scatter.dens.points)
+export(createReport)
+export(createReportGgPlot)
+export(createReportPlot)
+export(data.frame2GRanges)
+export(deviation.plot.beta)
+export(estimateProportionsCP)
+export(exportDMRs2regionFile)
+export(get.adjustment.variables)
+export(get.comparison.info)
+export(get.covariates.ct)
+export(get.covariates.sva)
+export(get.cpg.stats)
+export(get.files)
+export(greedycut.filter.matrix)
+export(greedycut.get.statistics)
+export(greedycut.get.submatrix)
+export(has.covariates.ct)
+export(has.covariates.sva)
+export(limmaP)
+export(load.region.subsegment.annotation)
+export(load.rnb.diffmeth)
+export(load.rnb.set)
+export(logger.argument)
+export(logger.close)
+export(logger.completed)
+export(logger.error)
+export(logger.getfiles)
+export(logger.info)
+export(logger.isinitialized)
+export(logger.machine.name)
+export(logger.start)
+export(logger.status)
+export(logger.validate.file)
+export(logger.warning)
+export(parallel.getNumWorkers)
+export(parallel.isEnabled)
+export(parallel.setup)
+export(parallel.teardown)
+export(performEnrichment.diffMeth)
+export(performGOenrichment.diffMeth.entrez)
+export(read.GS.report)
+export(read.bed.files)
+export(read.data.dir)
+export(read.geo)
+export(read.idat.files)
+export(read.sample.annotation)
+export(refFreeEWASP)
+export(rnb.RnBSet.to.GRangesList)
+export(rnb.RnBSet.to.bed)
+export(rnb.RnBSet.to.bedGraph)
+export(rnb.add.figure)
+export(rnb.add.list)
+export(rnb.add.paragraph)
+export(rnb.add.reference)
+export(rnb.add.section)
+export(rnb.add.table)
+export(rnb.add.tables)
+export(rnb.annotation.size)
+export(rnb.annotation2data.frame)
+export(rnb.beta2mval)
+export(rnb.build.index)
+export(rnb.color.legends)
+export(rnb.execute.batch.qc)
+export(rnb.execute.batcheffects)
+export(rnb.execute.clustering)
+export(rnb.execute.clustering.all)
+export(rnb.execute.computeDiffMeth)
+export(rnb.execute.context.removal)
+export(rnb.execute.ct.estimation)
+export(rnb.execute.dreduction)
+export(rnb.execute.export.csv)
+export(rnb.execute.filter.summary)
+export(rnb.execute.gender.prediction)
+export(rnb.execute.greedycut)
+export(rnb.execute.high.coverage.removal)
+export(rnb.execute.import)
+export(rnb.execute.low.coverage.masking)
+export(rnb.execute.na.removal)
+export(rnb.execute.normalization)
+export(rnb.execute.quality)
+export(rnb.execute.sex.removal)
+export(rnb.execute.snp.removal)
+export(rnb.execute.sva)
+export(rnb.execute.tnt)
+export(rnb.execute.variability.removal)
+export(rnb.export.all.annotation)
+export(rnb.export.annotation)
+export(rnb.export.to.ewasher)
+export(rnb.export.to.trackhub)
+export(rnb.find.relative.site.coord)
+export(rnb.get.annotation)
+export(rnb.get.assemblies)
+export(rnb.get.chromosomes)
+export(rnb.get.directory)
+export(rnb.get.mapping)
+export(rnb.get.reference)
+export(rnb.get.reliability.matrix)
+export(rnb.getOption)
+export(rnb.infinium.control.targets)
+export(rnb.initialize.reports)
+export(rnb.is.option)
+export(rnb.load.annotation)
+export(rnb.load.sitelist)
+export(rnb.message.plot)
+export(rnb.mval2beta)
+export(rnb.options)
+export(rnb.options2xml)
+export(rnb.performance.profile)
+export(rnb.plot.beta.comparison)
+export(rnb.plot.betadistribution.probeCategories)
+export(rnb.plot.betadistribution.sampleGroups)
+export(rnb.plot.biseq.coverage)
+export(rnb.plot.biseq.coverage.hist)
+export(rnb.plot.biseq.coverage.violin)
+export(rnb.plot.control.barplot)
+export(rnb.plot.control.boxplot)
+export(rnb.plot.coverage.thresholds)
+export(rnb.plot.ct.heatmap)
+export(rnb.plot.dreduction)
+export(rnb.plot.locus.profile)
+export(rnb.plot.marker.fstat)
+export(rnb.plot.negative.boxplot)
+export(rnb.plot.num.sites.covg)
+export(rnb.plot.pheno.categories)
+export(rnb.plot.region.profile.density)
+export(rnb.plot.region.profiles)
+export(rnb.plot.region.site.density)
+export(rnb.plot.sentrix.distribution)
+export(rnb.plot.sentrix.distributions)
+export(rnb.plot.snp.barplot)
+export(rnb.plot.snp.boxplot)
+export(rnb.plot.snp.heatmap)
+export(rnb.region.types)
+export(rnb.region.types.for.analysis)
+export(rnb.remove.annotation)
+export(rnb.run.analysis)
+export(rnb.run.differential)
+export(rnb.run.example)
+export(rnb.run.exploratory)
+export(rnb.run.import)
+export(rnb.run.inference)
+export(rnb.run.preprocessing)
+export(rnb.run.qc)
+export(rnb.run.tnt)
+export(rnb.run.xml)
+export(rnb.sample.groups)
+export(rnb.sample.replicates)
+export(rnb.sample.summary.table)
+export(rnb.save.annotation)
+export(rnb.set.annotation)
+export(rnb.set.annotation.and.cpg.stats)
+export(rnb.show.report)
+export(rnb.step.betadistribution)
+export(rnb.write.table)
+export(rnb.xml2options)
+export(rowOneSampleTP)
+export(rowPairedTP)
+export(rowWelchP)
+export(save.rnb.diffmeth)
+export(save.rnb.set)
+export(set.covariates.ct)
+export(set.covariates.sva)
+exportClasses(ClusterArchitecture)
+exportClasses(Report)
+exportClasses(ReportGgPlot)
+exportClasses(ReportPlot)
+exportClasses(RnBClusterRun)
+exportClasses(RnBDiffMeth)
+exportClasses(RnBSet)
+exportClasses(RnBeadClustering)
+exportClasses(RnBeadRawSet)
+exportClasses(RnBeadSet)
+exportClasses(RnBiseqSet)
+exportMethods(M)
+exportMethods(U)
+exportMethods(addDiffMethTable)
+exportMethods(addPheno)
+exportMethods(annotation)
+exportMethods(assembly)
+exportMethods(combine)
+exportMethods(covg)
+exportMethods(destroy)
+exportMethods(dpval)
+exportMethods(get.comparison.grouplabels)
+exportMethods(get.comparison.groupsizes)
+exportMethods(get.comparisons)
+exportMethods(get.covg.thres)
+exportMethods(get.region.types)
+exportMethods(get.site.test.method)
+exportMethods(get.table)
+exportMethods(getExecutable)
+exportMethods(getModuleNumCores)
+exportMethods(getSubCmdStr)
+exportMethods(getSubCmdTokens)
+exportMethods(initialize)
+exportMethods(is.valid)
+exportMethods(join.diffMeth)
+exportMethods(mergeSamples)
+exportMethods(meth)
+exportMethods(mval)
+exportMethods(off)
+exportMethods(pheno)
+exportMethods(qc)
+exportMethods(regionMapping)
+exportMethods(regions)
+exportMethods(reload)
+exportMethods(remove.samples)
+exportMethods(remove.sites)
+exportMethods(run)
+exportMethods(samples)
+exportMethods(save.tables)
+exportMethods(setExecutable)
+exportMethods(setModuleNumCores)
+exportMethods(setModuleResourceRequirements)
+exportMethods(sites)
+exportMethods(summarize.regions)
+exportMethods(summarized.regions)
+exportMethods(updateRegionSummaries)
+import(BiocGenerics)
+import(GenomicRanges)
+import(IRanges)
+import(MASS)
+import(RColorBrewer)
+import(cluster)
+import(ff)
+import(fields)
+import(ggplot2)
+import(gridExtra)
+import(limma)
+import(matrixStats)
+import(methods)
+import(methylumi)
+importFrom(gplots,colorpanel)
+importFrom(gplots,heatmap.2)
+importFrom(illuminaio,readIDAT)
+importFrom(plyr,rbind.fill)