API for grandR
Comprehensive Analysis of Nucleotide Conversion Sequencing Data
| Global functions | |
|---|---|
| AddAnalysis | Man page |
| AddGenePlot | Man page |
| AddGlobalPlot | Man page |
| AddSlot | Man page Source code |
| Analyses | Man page |
| AnalyzeGeneSets | Man page Source code |
| ApplyContrasts | Man page Source code |
| CalibrateEffectiveLabelingTimeKineticFit | Man page Source code |
| CalibrateEffectiveLabelingTimeMatchHalflives | Man page |
| ClassifyGenes | Man page Source code |
| Coldata | Man page Source code |
| Coldata<- | Man page |
| Columns | Man page Source code |
| ComputeAbsolute | Man page Source code |
| ComputeColumnStatistics | Man page Source code |
| ComputeExpressionPercentage | Man page Source code |
| ComputeNonConstantParam | Man page Source code |
| ComputeNtrCI | Man page Source code |
| ComputeNtrPosteriorLower | Man page Source code |
| ComputeNtrPosteriorQuantile | Man page Source code |
| ComputeNtrPosteriorUpper | Man page Source code |
| ComputePseudoNtr | Man page Source code |
| ComputeSteadyStateHalfLives | Man page Source code |
| ComputeSummaryStatistics | Man page Source code |
| ComputeTotalExpression | Man page Source code |
| Condition | Man page Source code |
| Condition<- | Man page |
| Correct4sUDropoutHLFactor | Man page Source code |
| Correct4sUDropoutHLSpline | Man page Source code |
| CreateConvolutionTable | Man page Source code |
| CreatePdfs | Man page |
| CreatePdfsComparison | Man page |
| CreatePdfsParameters | Man page |
| CreatePdfsProfiles | Man page |
| CreatePseudobulkTable | Man page Source code |
| CreateWindows | Source code |
| DESeq2BIC | Man page Source code |
| DefaultSlot | Man page Source code |
| DefaultSlot<- | Man page |
| Defer | Man page |
| Design | Man page |
| DesignSemantics | Man page Source code |
| DropAnalysis | Man page |
| DropPlots | Man page |
| DropSlot | Man page Source code |
| Estimate4sUDropoutPercentage | Man page Source code |
| Estimate4sUDropoutPercentageForSample | Man page Source code |
| EstimateRegulation | Man page Source code |
| EvaluateNonConstantParam | Man page Source code |
| FilterGenes | Man page Source code |
| FindReferences | Man page Source code |
| Findno4sUPairs | Man page Source code |
| FitKinetics | Man page Source code |
| FitKineticsGeneLeastSquares | Man page Source code |
| FitKineticsGeneLogSpaceLinear | Man page Source code |
| FitKineticsGeneNtr | Man page Source code |
| FitKineticsGeneSnapshot | Man page |
| FitKineticsPulseR | Man page Source code |
| FitKineticsSnapshot | Man page |
| FormatCorrelation | Man page Source code |
| GeneInfo | Man page Source code |
| GeneInfo<- | Man page |
| Genes | Man page Source code |
| GetAnalysisTable | Man page |
| GetContrasts | Man page |
| GetContrasts.default | Man page Source code |
| GetContrasts.grandR | Man page Source code |
| GetData | Man page Source code |
| GetDiagnosticParameters | Man page Source code |
| GetMatrix | Man page Source code |
| GetPairContrasts | Man page Source code |
| GetSignificantGenes | Man page Source code |
| GetSummarizeMatrix | Man page |
| GetSummarizeMatrix.default | Man page Source code |
| GetSummarizeMatrix.grandR | Man page Source code |
| GetTable | Man page Source code |
| GetTableQC | Source code |
| InitWindows | Source code |
| IsParallel | Man page |
| IsSparse | Man page Source code |
| LFC | Man page Source code |
| LikelihoodRatioTest | Man page Source code |
| ListGeneSets | Man page Source code |
| MAPlot | Man page |
| Make4sUDropoutTable | Source code |
| MakeColdata | Man page Source code |
| Metadata | Man page Source code |
| Normalize | Man page Source code |
| NormalizeBaseline | Man page Source code |
| NormalizeEffectiveLabeling | Source code |
| NormalizeFPKM | Man page Source code |
| NormalizeRPM | Man page Source code |
| NormalizeTPM | Man page Source code |
| Pairwise | Man page Source code |
| PairwiseDESeq2 | Man page Source code |
| Plot4sUDropout | Man page |
| Plot4sUDropoutAll | Man page Source code |
| Plot4sUDropoutDeferAll | Man page Source code |
| Plot4sUDropoutRank | Man page Source code |
| Plot4sUDropoutRankAll | Man page Source code |
| Plot4sUDropoutRankDeferAll | Man page Source code |
| PlotAnalyses | Man page |
| PlotConversionFreq | Man page |
| PlotGene | Man page |
| PlotGeneGroupsBars | Man page |
| PlotGeneGroupsPoints | Man page |
| PlotGeneOldVsNew | Man page |
| PlotGeneProgressiveTimecourse | Man page |
| PlotGeneSnapshotTimecourse | Man page |
| PlotGeneTotalVsNtr | Man page |
| PlotGlobal | Man page |
| PlotHeatmap | Man page Source code |
| PlotMismatchPositionForSample | Man page Source code |
| PlotMismatchPositionForType | Man page Source code |
| PlotModelCompareConv | Man page |
| PlotModelCompareErr | Man page |
| PlotModelCompareErrPrior | Man page |
| PlotModelCompareLL | Man page |
| PlotModelCompareNtr | Man page |
| PlotModelConv | Man page |
| PlotModelErr | Man page |
| PlotModelLabelTimeCourse | Man page |
| PlotModelNtr | Man page |
| PlotModelShape | Man page |
| PlotPCA | Man page Source code |
| PlotProfileLikelihood | Man page |
| PlotScatter | Man page Source code |
| PlotSimulation | Man page |
| PlotTypeDistribution | Man page |
| Plots | Man page |
| PoolColumns | Man page Source code |
| ROPE.LFC | Source code |
| ReadCounts | Man page Source code |
| ReadFeatureCounts | Man page Source code |
| ReadGRAND | Man page Source code |
| ReadGRAND3 | Man page Source code |
| ReadGRAND3_dense | Source code |
| ReadGRAND3_sparse | Source code |
| ReadNewTotal | Man page Source code |
| ReadOldMixMatrices | Source code |
| RenameColumns | Man page Source code |
| RotatateAxisLabels | Man page |
| SaveNtrSlot | Man page Source code |
| Scale | Man page Source code |
| Semantics.concentration | Man page Source code |
| Semantics.time | Man page Source code |
| ServeGrandR | Man page Source code |
| SetParallel | Man page |
| SimulateKinetics | Man page |
| SimulateReadsForSample | Man page Source code |
| SimulateTimeCourse | Man page Source code |
| SimulateTimeCourseNonConstant | Man page |
| Slots | Man page Source code |
| Summarize | Man page Source code |
| SwapColumns | Man page Source code |
| Title | Man page Source code |
| ToIndex | Man page Source code |
| Transform | Source code |
| Transform.VST | Man page Source code |
| Transform.Z | Man page Source code |
| Transform.logFC | Man page Source code |
| Transform.no | Man page Source code |
| TransformSnapshot | Man page |
| UpdateSymbols | Man page Source code |
| UseNtrSlot | Man page Source code |
| VulcanoPlot | Man page |
| `Coldata<-` | Source code |
| `Condition<-` | Source code |
| `DefaultSlot<-` | Source code |
| `GeneInfo<-` | Source code |
| as.Seurat.grandR | Man page Source code |
| as.Seurat.legacy.grandR | Source code |
| as.grandR | Source code |
| balpha | Source code |
| bbeta | Source code |
| beta.approximate.mixture | Source code |
| bmean | Source code |
| bquote.pval | Source code |
| bvar | Source code |
| check.analysis | Man page Source code |
| check.and.make.unique | Source code |
| check.mode.slot | Man page Source code |
| check.slot | Man page Source code |
| comp.fpkm | Source code |
| comp.hl | Source code |
| comp.rpm | Source code |
| comp.tpm | Source code |
| correctdropout | Man page |
| data.apply | Man page Source code |
| dbinommix | Source code |
| density2d | Man page Source code |
| dim.grandR | Man page Source code |
| dimnames.grandR | Man page Source code |
| dropout | Man page |
| dropoutpercent | Man page |
| dtbbinom | Source code |
| dtbbinommix | Source code |
| dtbeta | Source code |
| ebinom | Source code |
| ebinommix | Source code |
| estimate.dispersion | Man page |
| etbbinom | Source code |
| etbbinommix | Source code |
| etbeta | Source code |
| f.new | Man page Source code |
| f.nonconst | Man page Source code |
| f.nonconst.linear | Man page Source code |
| f.old.equi | Man page Source code |
| f.old.nonequi | Man page Source code |
| get.mode.slot | Man page Source code |
| grandR | Man page Source code |
| hierarchical.beta.posterior | Source code |
| ibeta | Source code |
| is.binom | Source code |
| is.grandR | Man page Source code |
| is.tbbinom | Source code |
| kinetics2vector | Man page |
| libeta | Source code |
| logLik_grmodel | Source code |
| logdiff | Source code |
| lse | Source code |
| lsse | Source code |
| make.continuous.colors | Source code |
| merge.grandR | Man page Source code |
| merge_columns | Source code |
| merge_genes | Source code |
| model.par | Source code |
| model.par.empty | Source code |
| plapply | Man page |
| print.grandR | Man page Source code |
| print_grmodel | Source code |
| psapply | Man page |
| ptbeta | Source code |
| qtbeta | Source code |
| rbinommix | Source code |
| read.grand.internal | Source code |
| read.tsv | Source code |
| rtbbinom | Source code |
| rtbbinommix | Source code |
| rtbeta | Source code |
| smartrbind | Source code |
| split.grandR | Man page Source code |
| structure2vector | Man page |
| subset.grandR | Man page Source code |
| tabrbinommix | Source code |
| tabrtbbinommix | Source code |
| try.file | Source code |
