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