# Revealing Splicing Dynamics at Single-Cell Resolution

## Documentation for package ‘MARVEL’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
AnnotateGenes.10x | Annotate splice junctions
AnnotateSJ.10x | Annotate splice junctions
AnnoVolcanoPlot | Annotate volcano plot with nonsense-mediated decay (NMD) genes
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