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 |