Analyses                Analysis table functions
AnalyzeGeneSets         Gene set analysis
ApplyContrasts          Apply a function over contrasts
CalibrateEffectiveLabelingTimeKineticFit
                        Uses the kinetic model to calibrate the
                        effective labeling time.
CalibrateEffectiveLabelingTimeMatchHalflives
                        Calibrate the effective labeling time by
                        matching half-lives to a .reference
ClassifyGenes           Build the type column for the gene info table.
Coldata                 Get the column annotation table or add
                        additional columns to it
ComputeColumnStatistics
                        Compute statistics for all columns (i.e.
                        samples or cells)
ComputeExpressionPercentage
                        Expression percentage computation
ComputeNonConstantParam
                        Compute and evaluate functions for non constant
                        rates
ComputeNtrPosteriorQuantile
                        Compute NTR quantiles
ComputePseudoNtr        Compute pseudo NTRs from two count matrices
ComputeSteadyStateHalfLives
                        Steady state half-lives for each sample
ComputeSummaryStatistics
                        Compute summary statistics
ComputeTotalExpression
                        Total expression computation
Condition               Get or set the conditions in the column
                        annotation table.
CreateConvolutionTable
                        Create Convolution Table from a Seurat object
CreatePdfs              Convencience methods for creating QC pdfs
CreatePseudobulkTable   Create Pseudobulk Table from a Seurat object
DESeq2BIC               Compute the Bayesian information criterion
                        (BIC)
DefaultSlot             Get or set the default slot for a grandR
                        object.
Defer                   Defer calling a function
Design                  A list of predefined names for design vectors
DesignSemantics         Build the design semantics list
EstimateRegulation      Estimate regulation from snapshot experiments
FilterGenes             Filter genes
FindReferences          Obtain reference columns (samples or cells) for
                        all columns (samples or cells) in the data set
Findno4sUPairs          Find equivalent no4sU samples for 4sU samples
FitKinetics             Fit kinetic models to all genes.
FitKineticsGeneLeastSquares
                        Fit a kinetic model according to non-linear
                        least squares.
FitKineticsGeneLogSpaceLinear
                        Fit a kinetic model using a linear model.
FitKineticsGeneNtr      Fit a kinetic model using the degradation rate
                        transformed NTR posterior distribution.
FitKineticsGeneSnapshot
                        Compute the posterior distributions of RNA
                        synthesis and degradation for a particular gene
FitKineticsPulseR       Fit kinetics using pulseR
FitKineticsSnapshot     Fits RNA kinetics from snapshot experiments
FormatCorrelation       Formatting function for correlations
GeneInfo                Get the gene annotation table or add additional
                        columns to it
Genes                   Gene and sample (or cell) names
GetAnalysisTable        Obtain a table of analysis results values
GetContrasts            Create a contrast matrix
GetData                 Obtain a tidy table of values for a gene or a
                        small set of genes
GetDiagnosticParameters
                        Describe parameters relevant to diagnostics
GetMatrix               Obtain a genes x values table as a large matrix
GetPairContrasts        Create a contrast matrix for two given
                        conditions
GetSignificantGenes     Significant genes
GetSummarizeMatrix      Create a summarize matrix
GetTable                Obtain a genes x values table
IsParallel              Checks for parallel execution
LFC                     Estimation of log2 fold changes
LikelihoodRatioTest     Compute a likelihood ratio test.
ListGeneSets            List available gene sets
MAPlot                  Make an MA plot
MakeColdata             Extract an annotation table from a formatted
                        names vector
Normalize               Normalization
NormalizeBaseline       Normalization to a baseline
Pairwise                Log2 fold changes and Wald tests for
                        differential expression
PairwiseDESeq2          Perform Wald tests for differential expression
PlotAnalyses            Convenience function to make the same type of
                        plot for multple analyses.
PlotConversionFreq      Diagnostic plot for conversion frequencies
PlotGeneGroupsBars      Plot gene values as bars
PlotGeneGroupsPoints    Plot gene groups as points
PlotGeneOldVsNew        Gene plot comparing old vs new RNA
PlotGeneProgressiveTimecourse
                        Plot progressive labeling timecourses
PlotGeneSnapshotTimecourse
                        Gene plot for snapshot timecourse data
PlotGeneTotalVsNtr      Gene plot comparing total RNA vs the NTR
PlotHeatmap             Create heatmaps from grandR objects
PlotMismatchPositionForSample
                        Diagnostic plot for mismatch position for
                        columns (by sample)
PlotMismatchPositionForType
                        Diagnostic plot for mismatch position for
                        columns (by mismatch type)
PlotModelCompareConv    Diagnostic plot for estimated models (global
                        conversion rate)
PlotModelCompareErr     Diagnostic plot for estimated models (global
                        error rate)
PlotModelCompareErrPrior
                        Diagnostic plot for estimated models (global
                        error rate)
PlotModelCompareLL      Diagnostic plot for estimated models (log
                        likelihoods)
PlotModelCompareNtr     Diagnostic plot for estimated models (global
                        NTR)
PlotModelConv           Diagnostic plot for estimated models (global
                        conversion rate)
PlotModelErr            Diagnostic plot for estimated models (global
                        error rate)
PlotModelLabelTimeCourse
                        Diagnostic plot for estimated models (4sU
                        increase)
PlotModelNtr            Diagnostic plot for estimated models (global
                        NTR)
PlotModelShape          Diagnostic plot for estimated models (global
                        shape parameter)
PlotPCA                 Make a PCA plot
PlotProfileLikelihood   Diagnostic plot for estimated models (global
                        error rate)
PlotScatter             Make a scatter plot
PlotSimulation          Plot simulated data
PlotTypeDistribution    Plot the distribution of gene types
Plots                   Stored plot functions
PoolColumns             Pool reads across columns
ReadCounts              Read a count table
ReadFeatureCounts       Read featureCounts
ReadGRAND               Read the output of GRAND-SLAM 2.0 into a grandR
                        object.
ReadGRAND3              Read the output of GRAND-SLAM 3.0 into a grandR
                        object.
ReadNewTotal            Read sparse new/total matrices
Renamer                 Create a renamer function
RotatateAxisLabels      Rotate x axis labels
SaveNtrSlot             Copy the NTR slot and save under new name
Scale                   Scale data
Semantics.concentration
                        Semantics for concentration columns
Semantics.time          Semantics for time columns
ServeGrandR             Serve a shiny web interface
SetParallel             Set up parallel execution
SimulateKinetics        Simulate the kinetics of old and new RNA for
                        given parameters.
SimulateReadsForSample
                        Simulate metabolic labeling - nucleotide
                        conversion RNA-seq data.
SimulateTimeCourse      Simulate a complete time course of metabolic
                        labeling - nucleotide conversion RNA-seq data.
SimulateTimeCourseNonConstant
                        Simulate a complete time course of metabolic
                        labeling - nucleotide conversion RNA-seq data.
Slots                   Slot functions
Summarize               Summarize a data matrix
ToIndex                 Obtain the indices of the given genes
Transform.no            Transformations for PlotHeatmap
TransformSnapshot       Estimate parameters for a one-shot experiment.
UpdateSymbols           Update symbols using biomaRt
UseNtrSlot              Use the given slot as NTR (is overwritten!)
VulcanoPlot             Make a Vulcano plot
Wilcoxon                Perform Wilcoxon tests for differential
                        expression
as.Seurat.grandR        Create Seurat object from a grandR object
check.analysis          Internal functions to check for a valid
                        analysis or slot names.
correctdropout          Correct for 4sU dropout
data.apply              Internal function to apply functions to all
                        slots etc.
density2d               Density estimation in 2d
dropout                 Perform 4sU dropout tests
dropoutpercent          Estimate 4sU dropout percentages
estimate.dispersion     Estimate dispersion parameters for a count
                        matrix using DESeq2
f.nonconst              Function to compute the abundance of new or old
                        RNA at time t for non-constant rates.
f.nonconst.linear       Function to compute the abundance of new or old
                        RNA at time t for non-constant rates.
f.old.equi              Functions to compute the abundance of new or
                        old RNA at time t.
get.mode.slot           Internal functions to parse mode.slot strings
grandR                  Create a grandR object and retrieve basic
                        information
psapply                 Parallel (s/l)apply
structure2vector        Convert a structure into a vector
