Revealing Splicing Dynamics at Single-Cell Resolution

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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