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MARVEL  

Revealing Splicing Dynamics at Single-Cell Resolution
View on CRAN: Click here


Download and install MARVEL package within the R console
Install from CRAN:
install.packages("MARVEL")

Install from Github:
library("remotes")
install_github("cran/MARVEL")

Install by package version:
library("remotes")
install_version("MARVEL", "1.4.0")



Attach the package and use:
library("MARVEL")
Maintained by
Sean Wen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-03-01
Latest Update: 2022-10-31
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.
How to cite:
Sean Wen (2021). MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution. R package version 1.4.0, https://cran.r-project.org/web/packages/MARVEL
Previous versions and publish date:
1.0.0 (2021-03-01 10:00), 1.1.0 (2021-03-31 12:40), 1.2.0 (2021-09-02 09:40), 1.2.1 (2021-09-15 07:30), 1.3.0 (2022-10-29 11:24)
Other packages that cited MARVEL R package
View MARVEL citation profile
Other R packages that MARVEL depends, imports, suggests or enhances
Functions, R codes and Examples using the MARVEL R package
Some associated functions: AnnoVolcanoPlot . AnnotateGenes.10x . AnnotateSJ.10x . AssignModality . BioPathways.10x . BioPathways.Plot.10x . BioPathways.Plot . BioPathways . CheckAlignment.10x . CheckAlignment.Exp . CheckAlignment.PSI.Exp . CheckAlignment.PSI . CheckAlignment.SJ . CheckAlignment . CompareExpr . CompareValues.Exp.Spliced . CompareValues.Exp . CompareValues.Genes.10x . CompareValues.PSI . CompareValues.SJ.10x . CompareValues . ComputePSI.A3SS . ComputePSI.A5SS . ComputePSI.AFE . ComputePSI.ALE . ComputePSI.MXE . ComputePSI.RI . ComputePSI.SE . ComputePSI . CountEvents . CreateMarvelObject.10x . CreateMarvelObject . DetectEvents.AFE.NegStrand . DetectEvents.AFE.PosStrand . DetectEvents.AFE . DetectEvents.ALE.NegStrand . DetectEvents.ALE.PosStrand . DetectEvents.ALE . DetectEvents . FilterGenes.10x . FindPTC.A3SS.NegStrand . FindPTC.A3SS.PosStrand . FindPTC.A5SS.NegStrand . FindPTC.A5SS.PosStrand . FindPTC.RI.NegStrand . FindPTC.RI.PosStrand . FindPTC.SE.NegStrand . FindPTC.SE.PosStrand . FindPTC . IsoSwitch.10x . IsoSwitch.PlotExpr . IsoSwitch . ModalityChange . ParseGTF . PctASE . PlotDEValues.Exp.Global . PlotDEValues.Exp.Spliced . PlotDEValues.Genes.10x . PlotDEValues.PSI.Distance . PlotDEValues.PSI.Mean.g2vsg1 . PlotDEValues.PSI.Mean . PlotDEValues.SJ.10x . PlotDEValues . PlotPctExprCells.Genes.10x . PlotPctExprCells.SJ.10x . PlotValues.Exp . PlotValues.PCA.CellGroup.10x . PlotValues.PCA.Gene.10x . PlotValues.PCA.PSI.10x . PlotValues.PSI . PlotValues . PropModality.Bar . PropModality.Doughnut . PropModality . PropPTC . RunPCA.Exp . RunPCA.PSI . RunPCA . SubsetCrypticA3SS . SubsetSamples . TransformExpValues . ValidateSJ.10x . adhocGene.DE.Gene.10x . adhocGene.DE.PSI.10x . adhocGene.PlotDEValues.10x . adhocGene.PlotSJPosition.10x . adhocGene.TabulateExpression.Gene.10x . adhocGene.TabulateExpression.PSI.10x . 
Some associated R codes: Script_DROPLET_01_CREATE_MARVEL_OBJECT.R . Script_DROPLET_02_PREPROCESS_1_AnnotateGenes.R . Script_DROPLET_02_PREPROCESS_2_AnnotateSJ.R . Script_DROPLET_02_PREPROCESS_3_ValidateSJ.R . Script_DROPLET_02_PREPROCESS_4_FilterGenes.R . Script_DROPLET_02_PREPROCESS_5_CheckAlignment.R . Script_DROPLET_03_EXPLORE_EXPRESSION_1_Gene.R . Script_DROPLET_03_EXPLORE_EXPRESSION_2_SJ.R . Script_DROPLET_04_DE_1_SJ.R . Script_DROPLET_04_DE_2_Gene.R . Script_DROPLET_04_DE_3_VolcanoPlot_SJ.R . Script_DROPLET_04_DE_4_VolcanoPlot_Gene.R . Script_DROPLET_05_DE_5_IsoSwitch.R . Script_DROPLET_05_DE_6_1_GO.R . Script_DROPLET_05_DE_6_2_GO_Plot.R . Script_DROPLET_07_ADHOC_PLOT_PCA_1_PlotFeatures.R . Script_DROPLET_07_ADHOC_PLOT_PCA_2_PlotValues_PSI.R . Script_DROPLET_07_ADHOC_PLOT_PCA_3_PlotValues_Gene.R . Script_DROPLET_09_ADHOC_GENE_1_TabulateExpression_Gene.R . Script_DROPLET_09_ADHOC_GENE_2_TabulateExpression_PSI.R . Script_DROPLET_09_ADHOC_GENE_3_DE_Gene.R . Script_DROPLET_09_ADHOC_GENE_4_DE_PSI.R . Script_DROPLET_09_ADHOC_GENE_5_PlotDEValues.R . Script_DROPLET_09_ADHOC_GENE_6_PlotSJPositions.R . Script_PLATE_01_CREATE_MARVEL_OBJECT.R . Script_PLATE_02_DETECT_EVENTS_0.R . Script_PLATE_02_DETECT_EVENTS_1_0_ALE.R . Script_PLATE_02_DETECT_EVENTS_1_1_ALE_PosStrand.R . Script_PLATE_02_DETECT_EVENTS_1_2_ALE_NegStrand.R . Script_PLATE_02_DETECT_EVENTS_2_0_AFE.R . Script_PLATE_02_DETECT_EVENTS_2_1_AFE_PosStrand.R . Script_PLATE_02_DETECT_EVENTS_2_2_AFE_NegStrand.R . Script_PLATE_03_COMPUTE_PSI_0_Compute.R . Script_PLATE_03_COMPUTE_PSI_1_Compute_SE.R . Script_PLATE_03_COMPUTE_PSI_2_Compute_MXE.R . Script_PLATE_03_COMPUTE_PSI_3_Compute_A5SS.R . Script_PLATE_03_COMPUTE_PSI_4_Compute_A3SS.R . Script_PLATE_03_COMPUTE_PSI_5_Compute_RI.R . Script_PLATE_03_COMPUTE_PSI_6_Compute_ALE.R . Script_PLATE_03_COMPUTE_PSI_7_Compute_AFE.R . Script_PLATE_04_PREPROCESS_2_SubsetSamples.R . Script_PLATE_04_PREPROCESS_3_0_CheckAlignment.R . Script_PLATE_04_PREPROCESS_3_1_CheckAlignment_PSI.R . Script_PLATE_04_PREPROCESS_3_2_CheckAlignment_Gene.R . Script_PLATE_04_PREPROCESS_3_3_CheckAlignment_PSI_Gene.R . Script_PLATE_04_PREPROCESS_3_4_CheckAlignment_SJ.R . Script_PLATE_04_PREPROCESS_4_TransformGeneValues.R . Script_PLATE_05_EVENTS_EXPRESSED.R . Script_PLATE_06_MODALITY_ANALYSIS_1_AssignModality.R . Script_PLATE_06_MODALITY_ANALYSIS_2_0_PropModality.R . Script_PLATE_06_MODALITY_ANALYSIS_2_1_PropModality_Doughnut.R . Script_PLATE_06_MODALITY_ANALYSIS_2_2_PropModality_Bar.R . Script_PLATE_07_PCA_0_RunPCA.R . Script_PLATE_07_PCA_1_RunPCA_PSI.R . Script_PLATE_07_PCA_2_RunPCA_Gene.R . Script_PLATE_08_DE_1_0_CompareValues.R . Script_PLATE_08_DE_1_2_CompareValues_PSI.R . Script_PLATE_08_DE_1_3_CompareValues_Gene.R . Script_PLATE_08_DE_1_4_CompareValues_SplicedGene.R . Script_PLATE_08_DE_1_5_SubsetCrypticA3SS.R . Script_PLATE_08_DE_2_0_PlotDEValues.R . Script_PLATE_08_DE_2_1_PlotDEValues_PSI_Distance.R . Script_PLATE_08_DE_2_2_PlotDEValues_PSI_Mean.R . Script_PLATE_08_DE_2_3_PlotDEValues_PSI_Mean_Group1vs2.R . Script_PLATE_08_DE_2_4_PlotDEValues_Gene_Mean_Global.R . Script_PLATE_08_DE_2_5_PlotDEValues_Gene_Mean_Spliced.R . Script_PLATE_08_DE_3_PctASE.R . Script_PLATE_08_DE_4_ModalityChange.R . Script_PLATE_08_DE_5_1_IsoSwitch.R . Script_PLATE_08_DE_5_2_IsoSwitch_PlotExpr.R . Script_PLATE_08_DE_6_1_GO.R . Script_PLATE_08_DE_6_2_GO_Plot.R . Script_PLATE_09_PREDICT_NMD_1_ParseGTF.R . Script_PLATE_09_PREDICT_NMD_2_0_FindPTC.R . Script_PLATE_09_PREDICT_NMD_2_1_FindPTC_SE_PosStrand.R . Script_PLATE_09_PREDICT_NMD_2_2_FindPTC_SE_NegStrand.R . Script_PLATE_09_PREDICT_NMD_3_1_FindPTC_RI_PosStrand.R . Script_PLATE_09_PREDICT_NMD_3_2_FindPTC_RI_NegStrand.R . Script_PLATE_09_PREDICT_NMD_4_1_FindPTC_A5SS_PosStrand.R . Script_PLATE_09_PREDICT_NMD_4_2_FindPTC_A5SS_NegStrand.R . Script_PLATE_09_PREDICT_NMD_5_1_FindPTC_A3SS_PosStrand.R . Script_PLATE_09_PREDICT_NMD_5_2_FindPTC_A3SS_NegStrand.R . Script_PLATE_09_PREDICT_NMD_6_PropPTC.R . Script_PLATE_09_PREDICT_NMD_7_CompareExpr.R . Script_PLATE_09_PREDICT_NMD_8_AnnoVolcanoPlot.R . Script_PLATE_10_ADHOC_PLOT_0_PlotValues.R . Script_PLATE_10_ADHOC_PLOT_1_PlotValues_PSI.R . Script_PLATE_10_ADHOC_PLOT_2_PlotValues_Gene.R .  Full MARVEL package functions and examples
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