Package: RnBeads 2.31.1
Fabian Mueller
RnBeads: RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Authors:
RnBeads_2.31.1.tar.gz
RnBeads_2.31.1.zip(r-4.7)RnBeads_2.31.1.zip(r-4.6)RnBeads_2.31.1.zip(r-4.5)
RnBeads_2.31.1.tgz(r-4.6-any)RnBeads_2.31.1.tgz(r-4.5-any)
RnBeads_2.31.1.tar.gz(r-4.7-any)RnBeads_2.31.1.tar.gz(r-4.6-any)
RnBeads_2.31.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RnBeads/json (API)
NEWS
| # Install 'RnBeads' in R: |
| install.packages('RnBeads', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- epic_v1_manifest - XenoMix EPICv1
- epic_v2_manifest - XenoMix EPICv2
- interspecies_probes_v1 - XenoMix interspeciesprobes
- interspecies_probes_v2 - XenoMix interspeciesprobes
- lump.hg19 - LUMP Support
- lump.hg38 - LUMP Support
On BioConductor:RnBeads-2.31.0(bioc 3.24)RnBeads-2.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
Last updated from:97064d7620. Checks:6 ERROR, 2 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 1467 | ||
| linux-devel-x86_64 | NOTE | 1802 | ||
| source / vignettes | OK | 1758 | ||
| linux-release-x86_64 | NOTE | 1804 | ||
| macos-release-arm64 | ERROR | 1573 | ||
| macos-oldrel-arm64 | ERROR | 1299 | ||
| windows-devel | ERROR | 1515 | ||
| windows-release | ERROR | 1488 | ||
| windows-oldrel | ERROR | 1492 | ||
| wasm-release | OK | 1478 |
Exports:addDiffMethTableaddPhenoaddRegionSubsegmentsannotationapply.iEVORAassemblyBMIQcombine.rnb.setscombineTestPvalsMethcomputeDiffTab.default.regioncomputeDiffTab.default.sitecomputeDiffTab.extended.sitecovgcreate.densityScattercreate.scatter.dens.pointscreateReportcreateReportGgPlotcreateReportPlotdata.frame2GRangesdestroydeviation.plot.betadiffVardownloadLolaDbsdpvalestimateProportionsCPexportDMRs2regionFilegenoget.adjustment.variablesget.comparison.grouplabelsget.comparison.groupsizesget.comparison.infoget.comparisonsget.covariates.ctget.covariates.svaget.covg.thresget.cpg.statsget.filesget.region.typesget.site.test.methodget.tableget.variability.methodgetCellTypesFromLolaDbgetExecutablegetModuleNumCoresgetNamesFromLolaDbgetSubCmdStrgetSubCmdTokensgetTargetFromLolaDbgreedycut.filter.matrixgreedycut.get.statisticsgreedycut.get.submatrixhas.covariates.cthas.covariates.svahasCovgincludes.sitesinitializeis.validisImputedjoin.diffMethlimmaPload.region.subsegment.annotationload.rnb.diffmethload.rnb.setloadLolaDbslogger.argumentlogger.closelogger.completedlogger.errorlogger.getfileslogger.infologger.isinitializedlogger.machine.namelogger.startlogger.statuslogger.validate.filelogger.warninglolaBarPlotlolaBoxPlotPerTargetlolaVolcanoPlotMmergeSamplesmethmvalnsitesoffparallel.getNumWorkersparallel.isEnabledparallel.setupparallel.teardownperformGoEnrichment.diffMethperformGOenrichment.diffMeth.entrezperformGOEnrichment.diffVarperformLolaEnrichment.diffMethperformLolaEnrichment.diffVarphenoprepareSOFTfileForGEOqcread.bed.filesread.data.dirread.GS.reportread.idat.filesread.sample.annotationread.single.bedrefFreeEWASPregionMappingregionsreloadremove.regionsremove.samplesremove.sitesrnb.add.figurernb.add.listrnb.add.paragraphrnb.add.referencernb.add.sectionrnb.add.tablernb.add.tablesrnb.annotation.sizernb.annotation2data.framernb.bed.from.segmentationrnb.beta2mvalrnb.boxplot.from.segmentationrnb.build.indexrnb.color.legendsrnb.combine.arraysrnb.combine.seqrnb.execute.age.predictionrnb.execute.batch.qcrnb.execute.batcheffectsrnb.execute.clusteringrnb.execute.clustering.allrnb.execute.computeDiffMethrnb.execute.context.removalrnb.execute.cross.reactive.removalrnb.execute.ct.estimationrnb.execute.diffVarrnb.execute.dreductionrnb.execute.export.csvrnb.execute.filter.summaryrnb.execute.genomewidernb.execute.greedycutrnb.execute.high.coverage.removalrnb.execute.high.dpval.maskingrnb.execute.importrnb.execute.imputationrnb.execute.low.coverage.maskingrnb.execute.lumprnb.execute.na.removalrnb.execute.normalizationrnb.execute.pOOBAHrnb.execute.qualityrnb.execute.segmentationrnb.execute.sex.predictionrnb.execute.sex.removalrnb.execute.snp.removalrnb.execute.svarnb.execute.tntrnb.execute.trainingrnb.execute.variability.removalrnb.export.all.annotationrnb.export.annotationrnb.export.to.ewasherrnb.export.to.trackhubrnb.find.relative.site.coordrnb.get.annotationrnb.get.assembliesrnb.get.chromosomesrnb.get.directoryrnb.get.mappingrnb.get.referencernb.get.reliability.matrixrnb.getOptionrnb.infinium.control.targetsrnb.initialize.reportsrnb.is.optionrnb.load.annotationrnb.load.annotation.from.dbrnb.load.sitelistrnb.message.plotrnb.mval2betarnb.optionsrnb.options2xmlrnb.performance.profilernb.plot.beta.comparisonrnb.plot.betadistribution.probeCategoriesrnb.plot.betadistribution.sampleGroupsrnb.plot.biseq.coveragernb.plot.biseq.coverage.histrnb.plot.biseq.coverage.violinrnb.plot.control.barplotrnb.plot.control.boxplotrnb.plot.coverage.thresholdsrnb.plot.ct.heatmaprnb.plot.dreductionrnb.plot.locus.profilernb.plot.marker.fstatrnb.plot.negative.boxplotrnb.plot.num.sites.covgrnb.plot.nv.heatmaprnb.plot.pheno.categoriesrnb.plot.region.profile.densityrnb.plot.region.profilesrnb.plot.region.site.densityrnb.plot.sentrix.distributionrnb.plot.sentrix.distributionsrnb.plot.snp.barplotrnb.plot.snp.boxplotrnb.plot.snp.heatmaprnb.read.geornb.region.typesrnb.region.types.for.analysisrnb.remove.annotationrnb.RnBSet.to.bedrnb.RnBSet.to.bedGraphrnb.RnBSet.to.GRangesListrnb.run_xenornb.run.analysisrnb.run.differentialrnb.run.djrnb.run.examplernb.run.exploratoryrnb.run.importrnb.run.inferencernb.run.preprocessingrnb.run.qcrnb.run.tntrnb.run.xmlrnb.sample.groupsrnb.sample.replicatesrnb.sample.summary.tablernb.save.annotationrnb.set.annotationrnb.set.annotation.and.cpg.statsrnb.show.reportrnb.step.betadistributionrnb.step.cnvrnb.write.tablernb.xml2optionsRnBeadRawSetRnBeadSetRnBiseqSetrowOneSampleTProwPairedTProwWelchPrunrun.cross.validationsave.rnb.diffmethsave.rnb.setsave.tablesset.covariates.ctset.covariates.svasetExecutablesetModuleNumCoressetModuleResourceRequirementssitessummarize.regionssummarized.regionsUupdateMethylationSitesupdateRegionSummaries
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcaToolscigarilloclicliprclustercodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdotCall64dplyrfarverfastmapFDb.InfiniumMethylation.hg19fffieldsfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgridExtragtablegtoolsh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimimeminfimulttestnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowspamSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract parts of BigFfMat | [,BigFfMat,ANY,ANY,ANY-method |
| Replace parts of BigFfMat | [<-,BigFfMat,ANY,ANY,ANY-method |
| RnBeads option values and restrictions | accepted current infos previous |
| addDiffMethTable-methods | addDiffMethTable addDiffMethTable,RnBDiffMeth-method |
| addPheno | addPheno addPheno,RnBSet-method |
| addRegionSubsegments | addRegionSubsegments |
| annotation-methods | annotation annotation,RnBSet-method |
| apply.iEVORA | apply.iEVORA |
| Conversion to/from RnBeadRawSet | as.RnBeadRawSet |
| assembly-methods | assembly assembly,RnBSet-method |
| auto.select.rank.cut | auto.select.rank.cut |
| BMIQ | BMIQ |
| ClusterArchitecture Class | ClusterArchitecture-class |
| ClusterArchitectureLSF Class | ClusterArchitectureLSF-class |
| ClusterArchitectureSGE Class | ClusterArchitectureSGE-class |
| ClusterArchitectureSLURM Class | ClusterArchitectureSLURM-class |
| as("RnBeadSet", "MethyLumiSet") | coercion-methods |
| cols.to.rank.site | cols.to.rank.region cols.to.rank.site |
| combine.diffMeth.objs | combine.diffMeth.objs |
| combine.rnb.sets-methods | combine.rnb.sets combine.rnb.sets,RnBSet,RnBSet-method combine.rnb.sets,RnBSet-method |
| combineTestPvalsMeth | combineTestPvalsMeth |
| computeDiffTab.region | computeDiffTab.default.region computeDiffTab.region |
| computeDiffTab.site | computeDiffTab.default.site computeDiffTab.extended.site computeDiffTab.site |
| covg-methods | covg covg,RnBSet-method |
| create.densityScatter | create.densityScatter |
| create.hex.summary.plot | create.hex.summary.plot |
| create.scatter.dens.points | create.scatter.dens.points |
| createReport | createReport |
| createReportGgPlot | createReportGgPlot |
| createReportPlot | createReportPlot |
| data.frame2GRanges | data.frame2GRanges |
| densRanks | densRanks |
| destroy-methods | destroy,RnBDiffMeth-method |
| destroy-methods | destroy destroy,RnBeadRawSet-method destroy,RnBeadSet-method destroy,RnBSet-method |
| deviation.plot.beta | deviation.plot.beta |
| diffVar | diffVar |
| Dimensions of BigFfMat | dim,BigFfMat-method |
| downloadLolaDbs | downloadLolaDbs |
| dpval-methods | dpval dpval,RnBeadSet-method |
| XenoMix EPICv1 (hg38) | epic_v1_manifest |
| XenoMix EPICv2 (hg38) | epic_v2_manifest |
| estimateProportionsCP | estimateProportionsCP |
| exportDMRs2regionFile | exportDMRs2regionFile |
| geno-methods | geno geno,RnBSet-method |
| get.adjustment.variables | get.adjustment.variables |
| get.comparison.grouplabels-methods | get.comparison.grouplabels get.comparison.grouplabels,RnBDiffMeth-method |
| get.comparison.groupsizes-methods | get.comparison.groupsizes get.comparison.groupsizes,RnBDiffMeth-method |
| get.comparison.info | get.comparison.info |
| get.comparisons-methods | get.comparisons get.comparisons,RnBDiffMeth-method |
| get.covariates.ct | get.covariates.ct |
| get.covariates.sva | get.covariates.sva |
| get.covg.thres-methods | get.covg.thres get.covg.thres,RnBDiffMeth-method |
| get.cpg.stats | get.cpg.stats |
| get.files | get.files |
| get.region.types-methods | get.region.types get.region.types,RnBDiffMeth-method |
| get.site.test.method-methods | get.site.test.method get.site.test.method,RnBDiffMeth-method |
| get.table-methods | get.table get.table,RnBDiffMeth-method |
| Returns the colum names of the differential variability table. | get.table.ids |
| get.variability.method-methods | get.variability.method get.variability.method,RnBDiffMeth-method |
| getCellTypesFromLolaDb | getCellTypesFromLolaDb |
| getExecutable-methods | getExecutable getExecutable,ClusterArchitecture,character-method getExecutable,ClusterArchitecture-method |
| getModuleNumCores-methods | getModuleNumCores getModuleNumCores,RnBClusterRun-method |
| getNamesFromLolaDb | getNamesFromLolaDb |
| getNumNaMeth-methods | getNumNaMeth getNumNaMeth,RnBSet-method |
| getSubCmdStr-methods | getSubCmdStr getSubCmdStr,ClusterArchitecture-method |
| getSubCmdTokens-methods | getSubCmdTokens getSubCmdTokens,ClusterArchitecture-method |
| getSubCmdTokens-methods | getSubCmdTokens,ClusterArchitectureLSF-method |
| getSubCmdTokens-methods | getSubCmdTokens,ClusterArchitectureSGE-method |
| getSubCmdTokens-methods | getSubCmdTokens,ClusterArchitectureSLURM-method |
| getTargetFromLolaDb | getTargetFromLolaDb |
| greedycut.filter.matrix | greedycut.filter.matrix |
| greedycut.get.statistics | greedycut.get.statistics |
| greedycut.get.submatrix | greedycut.get.submatrix |
| has.covariates.ct | has.covariates.ct |
| has.covariates.sva | has.covariates.sva |
| hasCovg-methods | hasCovg hasCovg,RnBSet-method |
| includes.sites-methods | includes.sites includes.sites,RnBDiffMeth-method |
| initialize.ClusterArchitecture | initialize,ClusterArchitecture-method |
| initialize.ClusterArchitectureLSF | initialize,ClusterArchitectureLSF-method |
| initialize.ClusterArchitectureSGE | initialize,ClusterArchitectureSGE-method |
| initialize.ClusterArchitectureSLURM | initialize,ClusterArchitectureSLURM-method |
| initialize.RnBClusterRun | initialize,RnBClusterRun-method |
| initialize.RnBDiffMeth | initialize,RnBDiffMeth-method |
| intensities.by.color | intensities.by.color |
| XenoMix interspeciesprobes (v1) | interspecies_probes_v1 |
| XenoMix interspeciesprobes (v2) | interspecies_probes_v2 |
| is.valid-methods | is.valid is.valid,RnBDiffMeth-method |
| isImputed | isImputed isImputed,RnBSet-method |
| join.diffMeth-methods | join.diffMeth join.diffMeth,RnBDiffMeth,RnBDiffMeth-method |
| limmaP | limmaP |
| load.region.subsegment.annotation | load.region.subsegment.annotation |
| load.rnb.diffmeth | load.rnb.diffmeth |
| load.rnb.set | load.rnb.set |
| loadLolaDbs | loadLolaDbs |
| logger.argument | logger.argument |
| logger.getfiles | logger.getfiles |
| logger.isinitialized | logger.isinitialized |
| logger.machine.name | logger.machine.name |
| Log File Management | logger.close logger.completed logger.start |
| Writing text messages to the log file. | logger.error logger.info logger.status logger.warning |
| logger.validate.file | logger.validate.file |
| lolaBarPlot | lolaBarPlot |
| lolaBoxPlotPerTarget | lolaBoxPlotPerTarget |
| lolaVolcanoPlot | lolaVolcanoPlot |
| LUMP Support | lump.hg19 |
| LUMP Support (hg38) | lump.hg38 |
| M-methods | M M,RnBeadRawSet-method |
| mask.sites.meth-methods | mask.sites.meth mask.sites.meth,RnBSet-method |
| mergeSamples | mergeSamples mergeSamples,RnBSet-method |
| meth-methods | meth meth,RnBSet-method |
| mval-methods | mval mval,RnBSet-method |
| nsites-methods | nsites nsites,RnBSet-method |
| off-methods | off off,Report-method off,ReportGgPlot-method off,ReportPlot-method |
| parallel.getNumWorkers | parallel.getNumWorkers |
| parallel.isEnabled | parallel.isEnabled |
| parallel.setup | parallel.setup |
| parallel.teardown | parallel.teardown |
| performGoEnrichment.diffMeth | performGoEnrichment.diffMeth |
| performGOenrichment.diffMeth.entrez | performGOenrichment.diffMeth.entrez |
| performGOEnrichment.diffVar | performGOEnrichment.diffVar |
| performLolaEnrichment.diffMeth | performLolaEnrichment.diffMeth |
| performLolaEnrichment.diffVar | performLolaEnrichment.diffVar |
| pheno-methods | pheno pheno,RnBSet-method |
| prepareSOFTfileForGEO | prepareSOFTfileForGEO |
| qc-methods | qc qc,RnBeadSet-method |
| read.bed.files | read.bed.files |
| read.data.dir | read.data.dir |
| read.GS.report | read.GS.report |
| read.idat.files | read.idat.files |
| read.idat.files2 | read.idat.files2 |
| read.sample.annotation | read.sample.annotation |
| read.single.bed | read.single.bed |
| refFreeEWASP | refFreeEWASP |
| regionMapping-methods | regionMapping regionMapping,RnBSet-method |
| regions-methods | regions regions,RnBSet-method |
| reload-methods | reload reload,RnBDiffMeth-method |
| remove.regions-methods | remove.regions remove.regions,RnBSet-method |
| remove.samples-methods | remove.samples remove.samples,RnBeadRawSet-method remove.samples,RnBeadSet-method remove.samples,RnBSet-method |
| remove.sites-methods | remove.sites remove.sites,RnBeadRawSet-method remove.sites,RnBeadSet-method remove.sites,RnBSet-method |
| Report Class | initialize,Report-method Report-class |
| ReportGgPlot Class | initialize,ReportGgPlot-method ReportGgPlot-class |
| ReportPlot Class | initialize,ReportPlot-method ReportPlot-class |
| rnb.add.figure | rnb.add.figure |
| rnb.add.list | rnb.add.list |
| rnb.add.paragraph | rnb.add.paragraph |
| rnb.add.reference | rnb.add.reference |
| rnb.add.section | rnb.add.section |
| rnb.add.table | rnb.add.table |
| rnb.add.tables | rnb.add.tables |
| rnb.annotation.size | rnb.annotation.size |
| rnb.annotation2data.frame | rnb.annotation2data.frame |
| rnb.bed.from.segmentation | rnb.bed.from.segmentation |
| rnb.beta2mval | rnb.beta2mval |
| rnb.boxplot.from.segmentation | rnb.boxplot.from.segmentation |
| rnb.build.index | rnb.build.index |
| rnb.call.destructor | rnb.call.destructor |
| rnb.color.legends | rnb.color.legends |
| Combine array-based datasets | rnb.combine.arrays |
| rnb.combine.seq | rnb.combine.seq |
| rnb.execute.age.prediction | rnb.execute.age.prediction |
| rnb.execute.batch.qc | rnb.execute.batch.qc |
| rnb.execute.batcheffects | rnb.execute.batcheffects |
| rnb.execute.clustering | rnb.execute.clustering |
| rnb.execute.clustering.all | rnb.execute.clustering.all |
| rnb.execute.computeDiffMeth | rnb.execute.computeDiffMeth |
| rnb.execute.context.removal | rnb.execute.context.removal |
| rnb.execute.cross.reactive.removal | rnb.execute.cross.reactive.removal |
| rnb.execute.ct.estimation | rnb.execute.ct.estimation |
| rnb.execute.diffVar | rnb.execute.diffVar |
| rnb.execute.dreduction | rnb.execute.dreduction |
| rnb.execute.export.csv | rnb.execute.export.csv |
| rnb.execute.filter.summary | rnb.execute.filter.summary |
| rnb.execute.gender.prediction | rnb.execute.gender.prediction |
| Genome-wide methylation level | rnb.execute.genomewide |
| rnb.execute.greedycut | rnb.execute.greedycut |
| rnb.execute.high.coverage.removal | rnb.execute.high.coverage.removal |
| rnb.execute.high.dpval.masking | rnb.execute.high.dpval.masking |
| rnb.execute.import | rnb.execute.import |
| rnb.execute.imputation | rnb.execute.imputation |
| rnb.execute.low.coverage.masking | rnb.execute.low.coverage.masking |
| Leukocytes unmethylation for purity | rnb.execute.lump |
| rnb.execute.na.removal | rnb.execute.na.removal |
| rnb.execute.normalization | rnb.execute.normalization |
| rnb.execute.pOOBAH | rnb.execute.pOOBAH |
| rnb.execute.quality | rnb.execute.quality |
| rnb.execute.segmentation | rnb.execute.segmentation |
| rnb.execute.sex.prediction | rnb.execute.sex.prediction |
| rnb.execute.sex.removal | rnb.execute.sex.removal |
| rnb.execute.snp.removal | rnb.execute.snp.removal |
| rnb.execute.sva | rnb.execute.sva |
| rnb.execute.tnt | rnb.execute.tnt |
| rnb.execute.training | rnb.execute.training |
| rnb.execute.variability.removal | rnb.execute.variability.removal |
| rnb.export.all.annotation | rnb.export.all.annotation |
| rnb.export.annotation | rnb.export.annotation |
| rnb.export.to.ewasher | rnb.export.to.ewasher |
| rnb.export.to.trackhub | rnb.export.to.trackhub |
| rnb.find.relative.site.coord | rnb.find.relative.site.coord |
| rnb.get.annotation | rnb.get.annotation |
| rnb.get.assemblies | rnb.get.assemblies |
| rnb.get.chromosomes | rnb.get.chromosomes |
| rnb.get.directory | rnb.get.directory |
| rnb.get.mapping | rnb.get.mapping |
| rnb.get.reference | rnb.get.reference |
| rnb.get.reliability.matrix | rnb.get.reliability.matrix |
| rnb.infinium.control.targets | rnb.infinium.control.targets |
| rnb.initialize.reports | rnb.initialize.reports |
| rnb.is.option | rnb.is.option |
| rnb.load.annotation | rnb.load.annotation |
| rnb.load.annotation.from.db | rnb.load.annotation.from.db |
| rnb.load.sitelist | rnb.load.sitelist |
| rnb.message.plot | rnb.message.plot |
| rnb.mval2beta | rnb.mval2beta |
| RnBeads Options | rnb.getOption rnb.options |
| rnb.options2xml | rnb.options2xml |
| rnb.performance.profile | rnb.performance.profile |
| rnb.plot.beta.comparison | rnb.plot.beta.comparison |
| rnb.plot.betadistribution.probeCategories | rnb.plot.betadistribution.probeCategories |
| rnb.plot.betadistribution.sampleGroups | rnb.plot.betadistribution.sampleGroups |
| rnb.plot.biseq.coverage | rnb.plot.biseq.coverage |
| rnb.plot.biseq.coverage.hist | rnb.plot.biseq.coverage.hist |
| rnb.plot.biseq.coverage.violin | rnb.plot.biseq.coverage.violin |
| rnb.plot.control.barplot | rnb.plot.control.barplot |
| rnb.plot.control.boxplot | rnb.plot.control.boxplot |
| rnb.plot.coverage.thresholds | rnb.plot.coverage.thresholds |
| rnb.plot.ct.heatmap | rnb.plot.ct.heatmap |
| rnb.plot.dreduction | rnb.plot.dreduction |
| rnb.plot.locus.profile | rnb.plot.locus.profile |
| rnb.plot.marker.fstat | rnb.plot.marker.fstat |
| rnb.plot.negative.boxplot | rnb.plot.negative.boxplot |
| rnb.plot.num.sites.covg | rnb.plot.num.sites.covg |
| rnb.plot.nv.heatmap | rnb.plot.nv.heatmap |
| rnb.plot.pheno.categories | rnb.plot.pheno.categories |
| rnb.plot.region.profiles | rnb.plot.region.profile.density |
| rnb.plot.region.profiles | rnb.plot.region.profiles |
| rnb.plot.region.site.density | rnb.plot.region.site.density |
| rnb.plot.sentrix.distribution | rnb.plot.sentrix.distribution |
| rnb.plot.sentrix.distributions | rnb.plot.sentrix.distributions |
| rnb.plot.snp.barplot | rnb.plot.snp.barplot |
| rnb.plot.snp.boxplot | rnb.plot.snp.boxplot |
| rnb.plot.snp.heatmap | rnb.plot.snp.heatmap |
| Import methylation data from GEO | rnb.read.geo |
| rnb.region.types | rnb.region.types |
| rnb.region.types.for.analysis | rnb.region.types.for.analysis |
| rnb.remove.annotation | rnb.remove.annotation |
| Export to BED files | rnb.RnBSet.to.bed |
| rnb.RnBSet.to.bedGraph | rnb.RnBSet.to.bedGraph |
| rnb.RnBSet.to.GRangesList | rnb.RnBSet.to.GRangesList |
| run_xeno | rnb.run_xeno |
| RnBeads Analysis Pipeline | rnb.run.analysis |
| rnb.run.dj | rnb.run.dj |
| rnb.run.example | rnb.run.example |
| RnBeads Modules in the Analysis Pipeline | rnb.run.differential rnb.run.exploratory rnb.run.import rnb.run.inference rnb.run.preprocessing rnb.run.qc rnb.run.tnt |
| rnb.run.xml | rnb.run.xml |
| rnb.sample.groups | rnb.sample.groups |
| rnb.sample.replicates | rnb.sample.replicates |
| rnb.sample.summary.table | rnb.sample.summary.table rnb.sample.summary.table,RnBSet-method |
| rnb.save.annotation | rnb.save.annotation |
| rnb.section.diffVar.region | rnb.section.diffVar.region |
| rnb.set.annotation | rnb.set.annotation |
| rnb.set.annotation.and.cpg.stats | rnb.set.annotation.and.cpg.stats |
| rnb.show.report | rnb.show.report |
| rnb.step.betadistribution | rnb.step.betadistribution |
| rnb.step.cnv | rnb.step.cnv |
| rnb.write.table | rnb.write.table |
| rnb.xml2options | rnb.xml2options |
| RnBClusterRun Class | RnBClusterRun-class |
| RnBDiffMeth Class | RnBDiffMeth-class |
| RnBeadClustering Class | initialize,RnBeadClustering-method RnBeadClustering-class |
| RnBeadRawSet-class | initialize,RnBeadRawSet-method RnBeadRawSet RnBeadRawSet-class |
| Analysis of genome-scale DNA methylation data with RnBeads | RnBeads-package RnBeads |
| RnBeads Annotation Tables | RnBeads.data |
| RnBeadSet Class | initialize,RnBeadSet-method RnBeadSet RnBeadSet-class |
| RnBiseqSet Class | initialize,RnBiseqSet-method RnBiseqSet RnBiseqSet-class |
| RnBSet Class | RnBSet-class |
| rowOneSampleTP | rowOneSampleTP |
| rowPairedTP | rowPairedTP |
| rowWelchP | rowWelchP |
| run-methods | run run,RnBClusterRun-method |
| run.cross.validation | run.cross.validation |
| sampleCovgApply-methods | sampleCovgApply sampleCovgApply,RnBSet-method |
| sampleMethApply-methods | sampleMethApply sampleMethApply,RnBSet-method |
| samples-methods | samples samples,RnBeadClustering-method samples,RnBSet-method |
| save.rnb.diffmeth | save.rnb.diffmeth |
| save.rnb.set | save.rnb.set |
| save.tables-methods | save.tables save.tables,RnBDiffMeth-method |
| set.covariates.ct | set.covariates.ct |
| set.covariates.sva | set.covariates.sva |
| setExecutable-methods | setExecutable setExecutable,ClusterArchitecture,character,character-method setExecutable,ClusterArchitecture-method |
| setModuleNumCores-methods | setModuleNumCores setModuleNumCores,RnBClusterRun,integer,character-method setModuleNumCores,RnBClusterRun-method |
| setModuleResourceRequirements-methods | setModuleResourceRequirements setModuleResourceRequirements,RnBClusterRun,character,character-method setModuleResourceRequirements,RnBClusterRun-method |
| sites-methods | sites sites,RnBSet-method |
| summarize.regions-methods | summarize.regions summarize.regions,RnBSet-method |
| summarized.regions-methods | summarized.regions summarized.regions,RnBSet-method |
| U-methods | U U,RnBeadRawSet-method |
| updateMethylationSites-methods | updateMethylationSites updateMethylationSites,RnBSet-method |
| updateRegionSummaries | updateRegionSummaries updateRegionSummaries,RnBSet-method |