Package: MARVEL 1.4.0

Sean Wen

MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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.

Authors:Sean Wen [aut, cre]

MARVEL_1.4.0.tar.gz
MARVEL_1.4.0.tar.gz(r-4.5-noble)MARVEL_1.4.0.tar.gz(r-4.4-noble)
MARVEL_1.4.0.tgz(r-4.4-emscripten)MARVEL_1.4.0.tgz(r-4.3-emscripten)
MARVEL.pdf |MARVEL.html✨
MARVEL/json (API)

# Install 'MARVEL' in R:
install.packages('MARVEL', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.71 score 51 scripts 203 downloads 88 exports 30 dependencies

Last updated 2 years agofrom:c01d756e9e. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-linuxOKOct 26 2024

Exports:adhocGene.DE.Gene.10xadhocGene.DE.PSI.10xadhocGene.PlotDEValues.10xadhocGene.PlotSJPosition.10xadhocGene.TabulateExpression.Gene.10xadhocGene.TabulateExpression.PSI.10xAnnotateGenes.10xAnnotateSJ.10xAnnoVolcanoPlotAssignModalityBioPathwaysBioPathways.10xBioPathways.PlotBioPathways.Plot.10xCheckAlignmentCheckAlignment.10xCheckAlignment.ExpCheckAlignment.PSICheckAlignment.PSI.ExpCheckAlignment.SJCompareExprCompareValuesCompareValues.ExpCompareValues.Exp.SplicedCompareValues.Genes.10xCompareValues.PSICompareValues.SJ.10xComputePSIComputePSI.A3SSComputePSI.A5SSComputePSI.AFEComputePSI.ALEComputePSI.MXEComputePSI.RIComputePSI.SECountEventsCreateMarvelObjectCreateMarvelObject.10xDetectEventsDetectEvents.AFEDetectEvents.AFE.NegStrandDetectEvents.AFE.PosStrandDetectEvents.ALEDetectEvents.ALE.NegStrandDetectEvents.ALE.PosStrandFilterGenes.10xFindPTCFindPTC.A3SS.NegStrandFindPTC.A3SS.PosStrandFindPTC.A5SS.NegStrandFindPTC.A5SS.PosStrandFindPTC.RI.NegStrandFindPTC.RI.PosStrandFindPTC.SE.NegStrandFindPTC.SE.PosStrandIsoSwitchIsoSwitch.10xIsoSwitch.PlotExprModalityChangeParseGTFPctASEPlotDEValuesPlotDEValues.Exp.GlobalPlotDEValues.Exp.SplicedPlotDEValues.Genes.10xPlotDEValues.PSI.DistancePlotDEValues.PSI.MeanPlotDEValues.PSI.Mean.g2vsg1PlotDEValues.SJ.10xPlotPctExprCells.Genes.10xPlotPctExprCells.SJ.10xPlotValuesPlotValues.ExpPlotValues.PCA.CellGroup.10xPlotValues.PCA.Gene.10xPlotValues.PCA.PSI.10xPlotValues.PSIPropModalityPropModality.BarPropModality.DoughnutPropPTCRunPCARunPCA.ExpRunPCA.PSISubsetCrypticA3SSSubsetSamplesTransformExpValuesValidateSJ.10x

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

MARVEL

Sean Wen

Rendered fromMARVEL.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2022-10-29
Started: 2021-03-01

Readme and manuals

Help Manual

Help pageTopics
Differential gene expression analysis of specified geneadhocGene.DE.Gene.10x
Differential splice junction analysis of specified geneadhocGene.DE.PSI.10x
Plot differential splice junction analysis results for a specified geneadhocGene.PlotDEValues.10x
Plots the locations of specified splice junction relative to isoformsadhocGene.PlotSJPosition.10x
Dotplot of gene expression values for a specified geneadhocGene.TabulateExpression.Gene.10x
Dotplot of splice junction expression values for a specified geneadhocGene.TabulateExpression.PSI.10x
Annotate splice junctionsAnnotateGenes.10x
Annotate splice junctionsAnnotateSJ.10x
Annotate volcano plot with nonsense-mediated decay (NMD) genesAnnoVolcanoPlot
Assign modalitiesAssignModality
Pathway enrichment analysisBioPathways
Pathway enrichment analysisBioPathways.10x
Plot pathway enrichment analysis resultsBioPathways.Plot
Plot pathway enrichment analysis resultsBioPathways.Plot.10x
Pre-flight checkCheckAlignment
Pre-flight checkCheckAlignment.10x
Check gene dataCheckAlignment.Exp
Check splicing dataCheckAlignment.PSI
Check splicing and gene data against each otherCheckAlignment.PSI.Exp
Check splice junction dataCheckAlignment.SJ
Compares gene expression changes based on nonsense-mediated decay (NMD) statusCompareExpr
Differential splicing and gene expression analysisCompareValues
Differential gene expression analysisCompareValues.Exp
Differential gene expression analysis for differentially spliced genesCompareValues.Exp.Spliced
Differential gene expression analysisCompareValues.Genes.10x
Differential splicing analysisCompareValues.PSI
Differential splice junction analysisCompareValues.SJ.10x
Compute percent spliced-in (PSI) valuesComputePSI
Compute Alternative 3' Splice Site (A3SS) Percent Spliced-in (PSI) ValuesComputePSI.A3SS
Compute alternative 5' splice site (A5SS) percent spliced-in (PSI) valuesComputePSI.A5SS
Compute alternative first exon (AFE) percent spliced-in (PSI) valuesComputePSI.AFE
Compute alternative last exon (ALE) percent spliced-in (PSI) valuesComputePSI.ALE
Compute mutually exclusive exons (MXE) percent spliced-in (PSI) valuesComputePSI.MXE
Compute retained-intron (RI) percent spliced-in (PSI) valuesComputePSI.RI
Compute skipped-exon (SE) percent spliced-in (PSI) valuesComputePSI.SE
Tabulate the number of expressed splicing eventsCountEvents
Create Marvel object for plate-based RNA-sequencing dataCreateMarvelObject
Create Marvel object for droplet-based RNA-sequencing dataCreateMarvelObject.10x
Detect Splicing EventsDetectEvents
Detect alternative first exonsDetectEvents.AFE
Detect alternative first exons on negative strandDetectEvents.AFE.NegStrand
Detect alternative first exons on positive strandDetectEvents.AFE.PosStrand
Detect alternative last exonsDetectEvents.ALE
Detect alternative last exons on negative strandDetectEvents.ALE.NegStrand
Detect alternative last exons on positive strandDetectEvents.ALE.PosStrand
Filter specific gene typesFilterGenes.10x
Find premature terminal codons (PTCs)FindPTC
Find premature terminal codon (PTC) for alternative 3' splice site (A3SS) located on the negative strand of the transcriptFindPTC.A3SS.NegStrand
Find premature terminal codon (PTC) for alternative 3' splice site (A3SS) located on the positive strand of the transcriptFindPTC.A3SS.PosStrand
Find premature terminal codon (PTC) for alternative 5' splice site (A5SS) located on the negative strand of the transcriptFindPTC.A5SS.NegStrand
Find premature terminal codon (PTC) for alternative 5' splice site (A5SS) located on the positive strand of the transcriptFindPTC.A5SS.PosStrand
Find premature terminal codon (PTC) for retained-intron (RI) located on the negative strand of the transcriptFindPTC.RI.NegStrand
Find premature terminal codon (PTC) for retained-Intron (RI) located on the positive strand of the transcriptFindPTC.RI.PosStrand
Find premature terminal codon (PTC) for skipped-exon (SE) located on the negative Strand of the yranscriptFindPTC.SE.NegStrand
Find premature terminal codon (PTC) for skipped-exon (SE) located on the positive strand of the transcriptFindPTC.SE.PosStrand
Classify gene-splicing relationshipIsoSwitch
Classify gene-splicing relationshipIsoSwitch.10x
Plot gene-splicing relative changeIsoSwitch.PlotExpr
Classify modality changesModalityChange
Parse gene transfer file (GTF)ParseGTF
Tabulate differentially spliced splicing eventPctASE
Plot differential splicing and gene expression analysis resultsPlotDEValues
Plot global differential gene expression analysis resultsPlotDEValues.Exp.Global
Plot differential gene expression analysis of differentially spliced genesPlotDEValues.Exp.Spliced
Plot differential gene analysis resultsPlotDEValues.Genes.10x
Plot differential splicing analysis results based on distance statistics.PlotDEValues.PSI.Distance
Plot differential splicing analysis results based on mean PSI differencePlotDEValues.PSI.Mean
Plot differential splicing analysis results based on mean PSI differencePlotDEValues.PSI.Mean.g2vsg1
Plot differential splice junction analysis resultsPlotDEValues.SJ.10x
Plot gene expression distributionPlotPctExprCells.Genes.10x
Plot splice junction expression distributionPlotPctExprCells.SJ.10x
Plot percent spliced-in (PSI) or gene expression valuesPlotValues
Plot gene expression valuesPlotValues.Exp
Annotate reduced dimension space with cell featurePlotValues.PCA.CellGroup.10x
Annotate reduced dimension space with gene expression valuesPlotValues.PCA.Gene.10x
Annotate reduced dimension space with PSI valuesPlotValues.PCA.PSI.10x
Plot percent spliced-in (PSI) valuesPlotValues.PSI
Tabulate modality proportionPropModality
Modality proportion broken down by event typePropModality.Bar
Overall modality proportionPropModality.Doughnut
Tabulate proportion of transcripts with PTCPropPTC
Principle component analysisRunPCA
Principle component analysis for gene DataRunPCA.Exp
Principle component analysis for splicing dataRunPCA.PSI
Differential gene expression analysis for differentially spliced genesSubsetCrypticA3SS
Subset samples (cells)SubsetSamples
Transform gene expression ValuesTransformExpValues
Validate splice junctionsValidateSJ.10x