# Generated by roxygen2: do not edit by hand

S3method("*",MixMatrix)
S3method("+",MixMatrix)
S3method("-",MixMatrix)
S3method("/",MixMatrix)
S3method("[",MixMatrix)
S3method(GetContrasts,default)
S3method(GetContrasts,grandR)
S3method(GetSummarizeMatrix,default)
S3method(GetSummarizeMatrix,grandR)
S3method(Seurat::as.Seurat,grandR)
S3method(dim,grandR)
S3method(dimnames,grandR)
S3method(merge,grandR)
S3method(print,grandR)
S3method(split,grandR)
S3method(subset,grandR)
export("Coldata<-")
export("Condition<-")
export("DefaultSlot<-")
export("GeneInfo<-")
export(AddAnalysis)
export(AddGenePlot)
export(AddGlobalPlot)
export(AddSlot)
export(Analyses)
export(AnalyzeGeneSets)
export(ApplyContrasts)
export(CalibrateEffectiveLabelingTimeKineticFit)
export(CalibrateEffectiveLabelingTimeMatchHalflives)
export(ClassifyGenes)
export(Coldata)
export(Columns)
export(ComputeAbsolute)
export(ComputeColumnStatistics)
export(ComputeExpressionPercentage)
export(ComputeNonConstantParam)
export(ComputeNtrCI)
export(ComputeNtrPosteriorLower)
export(ComputeNtrPosteriorQuantile)
export(ComputeNtrPosteriorUpper)
export(ComputePseudoNtr)
export(ComputeSteadyStateHalfLives)
export(ComputeSummaryStatistics)
export(ComputeTotalExpression)
export(Condition)
export(Correct4sUDropoutHLFactor)
export(Correct4sUDropoutHLSpline)
export(CreatePdfs)
export(CreatePdfsComparison)
export(CreatePdfsParameters)
export(CreatePdfsProfiles)
export(DESeq2BIC)
export(DefaultSlot)
export(Defer)
export(Design)
export(DesignSemantics)
export(DropAnalysis)
export(DropPlots)
export(DropSlot)
export(Estimate4sUDropoutPercentage)
export(Estimate4sUDropoutPercentageForSample)
export(EstimateRegulation)
export(EvaluateNonConstantParam)
export(FilterGenes)
export(FindReferences)
export(Findno4sUPairs)
export(FitKinetics)
export(FitKineticsGeneLeastSquares)
export(FitKineticsGeneLogSpaceLinear)
export(FitKineticsGeneNtr)
export(FitKineticsGeneSnapshot)
export(FitKineticsPulseR)
export(FitKineticsSnapshot)
export(FormatCorrelation)
export(GeneInfo)
export(Genes)
export(GetAnalysisTable)
export(GetContrasts)
export(GetData)
export(GetDiagnosticParameters)
export(GetMatrix)
export(GetPairContrasts)
export(GetSignificantGenes)
export(GetSummarizeMatrix)
export(GetTable)
export(IsParallel)
export(IsSparse)
export(LFC)
export(LikelihoodRatioTest)
export(ListGeneSets)
export(MAPlot)
export(MakeColdata)
export(Metadata)
export(Normalize)
export(NormalizeBaseline)
export(NormalizeFPKM)
export(NormalizeRPM)
export(NormalizeTPM)
export(Pairwise)
export(PairwiseDESeq2)
export(Plot4sUDropout)
export(Plot4sUDropoutAll)
export(Plot4sUDropoutDeferAll)
export(Plot4sUDropoutRank)
export(Plot4sUDropoutRankAll)
export(Plot4sUDropoutRankDeferAll)
export(PlotAnalyses)
export(PlotConversionFreq)
export(PlotGene)
export(PlotGeneGroupsBars)
export(PlotGeneGroupsPoints)
export(PlotGeneOldVsNew)
export(PlotGeneProgressiveTimecourse)
export(PlotGeneSnapshotTimecourse)
export(PlotGeneTotalVsNtr)
export(PlotGlobal)
export(PlotHeatmap)
export(PlotMismatchPositionForSample)
export(PlotMismatchPositionForType)
export(PlotModelCompareConv)
export(PlotModelCompareErr)
export(PlotModelCompareErrPrior)
export(PlotModelCompareLL)
export(PlotModelCompareNtr)
export(PlotModelConv)
export(PlotModelErr)
export(PlotModelLabelTimeCourse)
export(PlotModelNtr)
export(PlotModelShape)
export(PlotPCA)
export(PlotProfileLikelihood)
export(PlotScatter)
export(PlotSimulation)
export(PlotTypeDistribution)
export(Plots)
export(PoolColumns)
export(ReadCounts)
export(ReadFeatureCounts)
export(ReadGRAND)
export(ReadGRAND3)
export(ReadNewTotal)
export(RenameColumns)
export(RotatateAxisLabels)
export(SaveNtrSlot)
export(Scale)
export(Semantics.concentration)
export(Semantics.time)
export(ServeGrandR)
export(SetParallel)
export(SimulateKinetics)
export(SimulateReadsForSample)
export(SimulateTimeCourse)
export(SimulateTimeCourseNonConstant)
export(Slots)
export(Summarize)
export(SwapColumns)
export(Title)
export(ToIndex)
export(Transform.VST)
export(Transform.Z)
export(Transform.logFC)
export(Transform.no)
export(TransformSnapshot)
export(UpdateSymbols)
export(UseNtrSlot)
export(VulcanoPlot)
export(as.Seurat.grandR)
export(density2d)
export(estimate.dispersion)
export(f.new)
export(f.nonconst)
export(f.nonconst.linear)
export(f.old.equi)
export(f.old.nonequi)
export(grandR)
export(is.grandR)
export(kinetics2vector)
export(merge.grandR)
export(plapply)
export(psapply)
export(structure2vector)
import(ggplot2)
import(patchwork)
import(stats)
useDynLib(grandR, .registration = TRUE)
