Man pages for MARVEL
Revealing Splicing Dynamics at Single-Cell Resolution
| 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... |
| adhocGene.PlotSJPosition.10x | Plots the locations of specified splice junction relative to... |
| 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... |
| AnnotateGenes.10x | Annotate splice junctions |
| AnnotateSJ.10x | Annotate splice junctions |
| AnnoVolcanoPlot | Annotate volcano plot with nonsense-mediated decay (NMD)... |
| 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... |
| CompareValues | Differential splicing and gene expression analysis |
| CompareValues.Exp | Differential gene expression analysis |
| CompareValues.Exp.Spliced | Differential gene expression analysis for differentially... |
| 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... |
| ComputePSI.A5SS | Compute alternative 5' splice site (A5SS) percent spliced-in... |
| ComputePSI.AFE | Compute alternative first exon (AFE) percent spliced-in (PSI)... |
| ComputePSI.ALE | Compute alternative last exon (ALE) percent spliced-in (PSI)... |
| ComputePSI.MXE | Compute mutually exclusive exons (MXE) percent spliced-in... |
| 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... |
| FindPTC.A3SS.PosStrand | Find premature terminal codon (PTC) for alternative 3' splice... |
| FindPTC.A5SS.NegStrand | Find premature terminal codon (PTC) for alternative 5' splice... |
| FindPTC.A5SS.PosStrand | Find premature terminal codon (PTC) for alternative 5' splice... |
| FindPTC.RI.NegStrand | Find premature terminal codon (PTC) for retained-intron (RI)... |
| FindPTC.RI.PosStrand | Find premature terminal codon (PTC) for retained-Intron (RI)... |
| FindPTC.SE.NegStrand | Find premature terminal codon (PTC) for skipped-exon (SE)... |
| FindPTC.SE.PosStrand | Find premature terminal codon (PTC) for skipped-exon (SE)... |
| 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... |
| PlotDEValues.Exp.Global | Plot global differential gene expression analysis results |
| PlotDEValues.Exp.Spliced | Plot differential gene expression analysis of differentially... |
| PlotDEValues.Genes.10x | Plot differential gene analysis results |
| PlotDEValues.PSI.Distance | Plot differential splicing analysis results based on distance... |
| PlotDEValues.PSI.Mean | Plot differential splicing analysis results based on mean PSI... |
| PlotDEValues.PSI.Mean.g2vsg1 | Plot differential splicing analysis results based on mean PSI... |
| 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... |
| SubsetSamples | Subset samples (cells) |
| TransformExpValues | Transform gene expression Values |
| ValidateSJ.10x | Validate splice junctions |
