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MARVEL (version 1.4.0)

Revealing Splicing Dynamics at Single-Cell Resolution

Description

Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of software to investigate splicing dynamics at single-cell resolution. 'MARVEL' enables splicing analysis of single-cell RNA-sequencing data generated from plate- and droplet-based library preparation methods.

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Version

Install

install.packages('MARVEL')

Monthly Downloads

66

Version

1.4.0

License

GPL-3

Maintainer

Sean Wen

Last Published

October 31st, 2022

Functions in MARVEL (1.4.0)

AnnotateGenes.10x

Annotate splice junctions

AnnoVolcanoPlot

Annotate volcano plot with nonsense-mediated decay (NMD) genes

Annotate splice junctions

BioPathways.Plot.10x

Plot pathway enrichment analysis results

BioPathways.10x

Pathway enrichment analysis

CheckAlignment.Exp

Check gene data

CompareValues.Exp.Spliced

Differential gene expression analysis for differentially spliced genes

CompareValues.Genes.10x

Differential gene expression analysis

CheckAlignment.PSI.Exp

Check splicing and gene data against each other

CompareValues.PSI

Differential splicing analysis

CheckAlignment.SJ

Check splice junction data

Differential splicing and gene expression analysis

Pre-flight check

Compares gene expression changes based on nonsense-mediated decay (NMD) status

CompareValues.Exp

Differential gene expression analysis

CheckAlignment.PSI

Check splicing data

CompareValues.SJ.10x

Differential splice junction analysis

Compute skipped-exon (SE) percent spliced-in (PSI) values

Compute retained-intron (RI) percent spliced-in (PSI) values

ComputePSI.A5SS

Compute alternative 5' splice site (A5SS) percent spliced-in (PSI) values

Compute mutually exclusive exons (MXE) percent spliced-in (PSI) values

Compute percent spliced-in (PSI) values

ComputePSI.A3SS

Compute Alternative 3' Splice Site (A3SS) Percent Spliced-in (PSI) Values

Compute alternative last exon (ALE) percent spliced-in (PSI) values

Compute alternative first exon (AFE) percent spliced-in (PSI) values

Tabulate the number of expressed splicing events

CreateMarvelObject.10x

Create Marvel object for droplet-based RNA-sequencing data

CreateMarvelObject

Create Marvel object for plate-based RNA-sequencing data

DetectEvents.AFE.PosStrand

Detect alternative first exons on positive strand

DetectEvents.AFE.NegStrand

Detect alternative first exons on negative strand

DetectEvents.ALE

Detect alternative last exons

DetectEvents.ALE.PosStrand

Detect alternative last exons on positive strand

FilterGenes.10x

Filter specific gene types

Detect Splicing Events

FindPTC.SE.PosStrand

Find premature terminal codon (PTC) for skipped-exon (SE) located on the positive 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.A5SS.NegStrand

Find premature terminal codon (PTC) for alternative 5' splice site (A5SS) located on the negative strand of the transcript

Classify gene-splicing relationship

FindPTC.RI.PosStrand

Find premature terminal codon (PTC) for retained-Intron (RI) 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.SE.NegStrand

Find premature terminal codon (PTC) for skipped-exon (SE) located on the negative Strand of the yranscript

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

DetectEvents.ALE.NegStrand

Detect alternative last exons on negative strand

PlotDEValues.PSI.Distance

Plot differential splicing analysis results based on distance statistics.

DetectEvents.AFE

Detect alternative first exons

FindPTC.A3SS.PosStrand

Find premature terminal codon (PTC) for alternative 3' splice site (A3SS) located on the positive strand of the transcript

PlotDEValues.PSI.Mean

Plot differential splicing analysis results based on mean PSI difference

Classify modality changes

Parse gene transfer file (GTF)

Tabulate differentially spliced splicing event

PlotDEValues.Exp.Global

Plot global differential gene expression analysis results

Classify gene-splicing relationship

IsoSwitch.PlotExpr

Plot gene-splicing relative change

Plot percent spliced-in (PSI) values

PlotValues.PCA.PSI.10x

Annotate reduced dimension space with PSI values

Plot differential splicing and gene expression analysis results

PlotDEValues.PSI.Mean.g2vsg1

Plot differential splicing analysis results based on mean PSI difference

Plot gene expression values

PlotPctExprCells.SJ.10x

Plot splice junction expression distribution

PlotPctExprCells.Genes.10x

Plot gene expression distribution

PlotDEValues.SJ.10x

Plot differential splice junction analysis results

PlotValues.PCA.CellGroup.10x

Annotate reduced dimension space with cell feature

PlotDEValues.Exp.Spliced

Plot differential gene expression analysis of differentially spliced genes

PlotDEValues.Genes.10x

Plot differential gene analysis results

PlotValues.PCA.Gene.10x

Annotate reduced dimension space with gene expression values

Principle component analysis for splicing data

SubsetCrypticA3SS

Differential gene expression analysis for differentially spliced genes

Plot percent spliced-in (PSI) or gene expression values

PropModality.Doughnut

Overall modality proportion

Tabulate proportion of transcripts with PTC

Principle component analysis

Subset samples (cells)

Principle component analysis for gene Data

PropModality.Bar

Modality proportion broken down by event type

Tabulate modality proportion

Validate splice junctions

adhocGene.PlotSJPosition.10x

Plots the locations of specified splice junction relative to isoforms

adhocGene.PlotDEValues.10x

Plot differential splice junction analysis results for a specified gene

TransformExpValues

Transform gene expression Values

adhocGene.TabulateExpression.PSI.10x

Dotplot of splice junction expression values for a specified gene

adhocGene.DE.PSI.10x

Differential splice junction analysis of specified gene

adhocGene.TabulateExpression.Gene.10x

Dotplot of gene expression values for a specified gene

adhocGene.DE.Gene.10x

Differential gene expression analysis of specified gene

BioPathways.Plot

Plot pathway enrichment analysis results

Pathway enrichment analysis

CheckAlignment.10x

Pre-flight check

Assign modalities