AnnoVolcanoPlot         Annotate volcano plot with nonsense-mediated
                        decay (NMD) genes
AnnotateGenes.10x       Annotate splice junctions
AnnotateSJ.10x          Annotate splice junctions
AssignModality          Assign modalities
BioPathways             Pathway enrichment analysis
BioPathways.10x         Pathway enrichment analysis
BioPathways.Plot        Plot pathway enrichment analysis results
BioPathways.Plot.10x    Plot pathway enrichment analysis results
CheckAlignment          Pre-flight check
CheckAlignment.10x      Pre-flight check
CheckAlignment.Exp      Check gene data
CheckAlignment.PSI      Check splicing data
CheckAlignment.PSI.Exp
                        Check splicing and gene data against each other
CheckAlignment.SJ       Check splice junction data
CompareExpr             Compares gene expression changes based on
                        nonsense-mediated decay (NMD) status
CompareValues           Differential splicing and gene expression
                        analysis
CompareValues.Exp       Differential gene expression analysis
CompareValues.Exp.Spliced
                        Differential gene expression analysis for
                        differentially spliced genes
CompareValues.Genes.10x
                        Differential gene expression analysis
CompareValues.PSI       Differential splicing analysis
CompareValues.SJ.10x    Differential splice junction analysis
ComputePSI              Compute percent spliced-in (PSI) values
ComputePSI.A3SS         Compute Alternative 3' Splice Site (A3SS)
                        Percent Spliced-in (PSI) Values
ComputePSI.A5SS         Compute alternative 5' splice site (A5SS)
                        percent spliced-in (PSI) values
ComputePSI.AFE          Compute alternative first exon (AFE) percent
                        spliced-in (PSI) values
ComputePSI.ALE          Compute alternative last exon (ALE) percent
                        spliced-in (PSI) values
ComputePSI.MXE          Compute mutually exclusive exons (MXE) percent
                        spliced-in (PSI) values
ComputePSI.RI           Compute retained-intron (RI) percent spliced-in
                        (PSI) values
ComputePSI.SE           Compute skipped-exon (SE) percent spliced-in
                        (PSI) values
CountEvents             Tabulate the number of expressed splicing
                        events
CreateMarvelObject      Create Marvel object for plate-based
                        RNA-sequencing data
CreateMarvelObject.10x
                        Create Marvel object for droplet-based
                        RNA-sequencing data
DetectEvents            Detect Splicing Events
DetectEvents.AFE        Detect alternative first exons
DetectEvents.AFE.NegStrand
                        Detect alternative first exons on negative
                        strand
DetectEvents.AFE.PosStrand
                        Detect alternative first exons on positive
                        strand
DetectEvents.ALE        Detect alternative last exons
DetectEvents.ALE.NegStrand
                        Detect alternative last exons on negative
                        strand
DetectEvents.ALE.PosStrand
                        Detect alternative last exons on positive
                        strand
FilterGenes.10x         Filter specific gene types
FindPTC                 Find premature terminal codons (PTCs)
FindPTC.A3SS.NegStrand
                        Find premature terminal codon (PTC) for
                        alternative 3' splice site (A3SS) located on
                        the negative strand of the transcript
FindPTC.A3SS.PosStrand
                        Find premature terminal codon (PTC) for
                        alternative 3' splice site (A3SS) located on
                        the positive strand of the transcript
FindPTC.A5SS.NegStrand
                        Find premature terminal codon (PTC) for
                        alternative 5' splice site (A5SS) located on
                        the negative strand of the transcript
FindPTC.A5SS.PosStrand
                        Find premature terminal codon (PTC) for
                        alternative 5' splice site (A5SS) located on
                        the positive strand of the transcript
FindPTC.RI.NegStrand    Find premature terminal codon (PTC) for
                        retained-intron (RI) located on the negative
                        strand of the transcript
FindPTC.RI.PosStrand    Find premature terminal codon (PTC) for
                        retained-Intron (RI) located on the positive
                        strand of the transcript
FindPTC.SE.NegStrand    Find premature terminal codon (PTC) for
                        skipped-exon (SE) located on the negative
                        Strand of the yranscript
FindPTC.SE.PosStrand    Find premature terminal codon (PTC) for
                        skipped-exon (SE) located on the positive
                        strand of the transcript
IsoSwitch               Classify gene-splicing relationship
IsoSwitch.10x           Classify gene-splicing relationship
IsoSwitch.PlotExpr      Plot gene-splicing relative change
ModalityChange          Classify modality changes
ParseGTF                Parse gene transfer file (GTF)
PctASE                  Tabulate differentially spliced splicing event
PlotDEValues            Plot differential splicing and gene expression
                        analysis results
PlotDEValues.Exp.Global
                        Plot global differential gene expression
                        analysis results
PlotDEValues.Exp.Spliced
                        Plot differential gene expression analysis of
                        differentially spliced genes
PlotDEValues.Genes.10x
                        Plot differential gene analysis results
PlotDEValues.PSI.Distance
                        Plot differential splicing analysis results
                        based on distance statistics.
PlotDEValues.PSI.Mean   Plot differential splicing analysis results
                        based on mean PSI difference
PlotDEValues.PSI.Mean.g2vsg1
                        Plot differential splicing analysis results
                        based on mean PSI difference
PlotDEValues.SJ.10x     Plot differential splice junction analysis
                        results
PlotPctExprCells.Genes.10x
                        Plot gene expression distribution
PlotPctExprCells.SJ.10x
                        Plot splice junction expression distribution
PlotValues              Plot percent spliced-in (PSI) or gene
                        expression values
PlotValues.Exp          Plot gene expression values
PlotValues.PCA.CellGroup.10x
                        Annotate reduced dimension space with cell
                        feature
PlotValues.PCA.Gene.10x
                        Annotate reduced dimension space with gene
                        expression values
PlotValues.PCA.PSI.10x
                        Annotate reduced dimension space with PSI
                        values
PlotValues.PSI          Plot percent spliced-in (PSI) values
PropModality            Tabulate modality proportion
PropModality.Bar        Modality proportion broken down by event type
PropModality.Doughnut   Overall modality proportion
PropPTC                 Tabulate proportion of transcripts with PTC
RunPCA                  Principle component analysis
RunPCA.Exp              Principle component analysis for gene Data
RunPCA.PSI              Principle component analysis for splicing data
SubsetCrypticA3SS       Differential gene expression analysis for
                        differentially spliced genes
SubsetSamples           Subset samples (cells)
TransformExpValues      Transform gene expression Values
ValidateSJ.10x          Validate splice junctions
adhocGene.DE.Gene.10x   Differential gene expression analysis of
                        specified gene
adhocGene.DE.PSI.10x    Differential splice junction analysis of
                        specified gene
adhocGene.PlotDEValues.10x
                        Plot differential splice junction analysis
                        results for a specified gene
adhocGene.PlotSJPosition.10x
                        Plots the locations of specified splice
                        junction relative to isoforms
adhocGene.TabulateExpression.Gene.10x
                        Dotplot of gene expression values for a
                        specified gene
adhocGene.TabulateExpression.PSI.10x
                        Dotplot of splice junction expression values
                        for a specified gene
