Files in wenweixiong/MARVEL

Revealing Splicing Dynamics at Single-Cell Resolution

R/Script_DROPLET_01_CREATE_MARVEL_OBJECT.R R/Script_DROPLET_02_PREPROCESS_1_AnnotateGenes.R R/Script_DROPLET_02_PREPROCESS_2_AnnotateSJ.R R/Script_DROPLET_02_PREPROCESS_3_ValidateSJ.R R/Script_DROPLET_02_PREPROCESS_4_FilterGenes.R R/Script_DROPLET_02_PREPROCESS_5_CheckAlignment.R R/Script_DROPLET_03_EXPLORE_EXPRESSION_1_Gene.R R/Script_DROPLET_03_EXPLORE_EXPRESSION_2_SJ.R R/Script_DROPLET_04_DE_1_SJ.R R/Script_DROPLET_04_DE_2_Gene.R R/Script_DROPLET_04_DE_3_VolcanoPlot_SJ.R R/Script_DROPLET_04_DE_4_VolcanoPlot_Gene.R R/Script_DROPLET_05_DE_5_IsoSwitch.R R/Script_DROPLET_05_DE_6_1_GO.R R/Script_DROPLET_05_DE_6_2_GO_Plot.R R/Script_DROPLET_06_DE_PSEUDOBULK_1_SJ.R R/Script_DROPLET_07_ADHOC_PLOT_PCA_1_PlotFeatures.R R/Script_DROPLET_07_ADHOC_PLOT_PCA_2_PlotValues_PSI.R R/Script_DROPLET_07_ADHOC_PLOT_PCA_3_PlotValues_Gene.R R/Script_DROPLET_08_ADHOC_PLOT_BOXPLOT_1_PlotValues_PseudoBulk_PSI.R R/Script_DROPLET_08_ADHOC_PLOT_BOXPLOT_2_PlotValues_PseudoBulk_Gene.R R/Script_DROPLET_08_ADHOC_PLOT_HEATMAP_PlotValues_PSI_PseudoBulk.R R/Script_DROPLET_08_ADHOC_PLOT_VIOLINPLOT_PlotValues_SingleCell_Gene.R R/Script_DROPLET_09_ADHOC_GENE_1_TabulateExpression_Gene.R R/Script_DROPLET_09_ADHOC_GENE_2_TabulateExpression_PSI.R R/Script_DROPLET_09_ADHOC_GENE_3_DE_Gene.R R/Script_DROPLET_09_ADHOC_GENE_4_DE_PSI.R R/Script_DROPLET_09_ADHOC_GENE_5_PlotDEValues.R R/Script_DROPLET_09_ADHOC_GENE_6_PlotSJPositions.R R/Script_PLATE_00_rMATS_00_CreateFeatureData.R R/Script_PLATE_00_rMATS_01_CreateFeatureData_SE.R R/Script_PLATE_00_rMATS_02_CreateFeatureData_MXE.R R/Script_PLATE_00_rMATS_03_CreateFeatureData_RI.R R/Script_PLATE_00_rMATS_04_CreateFeatureData_A5SS.R R/Script_PLATE_00_rMATS_05_CreateFeatureData_A3SS.R R/Script_PLATE_00_rMATS_06_CreateBedFile_RI.R R/Script_PLATE_01_CREATE_MARVEL_OBJECT.R R/Script_PLATE_02_SUBSET_CRYPTIC_SS_0.R R/Script_PLATE_02_SUBSET_CRYPTIC_SS_1_A5SS.R R/Script_PLATE_02_SUBSET_CRYPTIC_SS_2_A3SS.R R/Script_PLATE_03_DETECT_EVENTS_0.R R/Script_PLATE_03_DETECT_EVENTS_1_0_ALE.R R/Script_PLATE_03_DETECT_EVENTS_1_1_ALE_PosStrand.R R/Script_PLATE_03_DETECT_EVENTS_1_2_ALE_NegStrand.R R/Script_PLATE_03_DETECT_EVENTS_2_0_AFE.R R/Script_PLATE_03_DETECT_EVENTS_2_1_AFE_PosStrand.R R/Script_PLATE_03_DETECT_EVENTS_2_2_AFE_NegStrand.R R/Script_PLATE_03_DETECT_EVENTS_3_0_RemoveCrypticSS.R R/Script_PLATE_03_DETECT_EVENTS_3_1_RemoveCrypticSS_ALE.R R/Script_PLATE_03_DETECT_EVENTS_3_2_RemoveCrypticSS_AFE.R R/Script_PLATE_04_COMPUTE_PSI_0_Compute.R R/Script_PLATE_04_COMPUTE_PSI_1_Compute_SE.R R/Script_PLATE_04_COMPUTE_PSI_2_Compute_MXE.R R/Script_PLATE_04_COMPUTE_PSI_3_Compute_A5SS.R R/Script_PLATE_04_COMPUTE_PSI_4_Compute_A3SS.R R/Script_PLATE_04_COMPUTE_PSI_5_Compute_RI.R R/Script_PLATE_04_COMPUTE_PSI_6_Compute_ALE.R R/Script_PLATE_04_COMPUTE_PSI_7_Compute_AFE.R R/Script_PLATE_04_COMPUTE_PSI_8_Compute_Posterior.R R/Script_PLATE_05_PREPROCESS_2_SubsetSamples.R R/Script_PLATE_05_PREPROCESS_3_0_CheckAlignment.R R/Script_PLATE_05_PREPROCESS_3_1_CheckAlignment_PSI.R R/Script_PLATE_05_PREPROCESS_3_2_CheckAlignment_Gene.R R/Script_PLATE_05_PREPROCESS_3_3_CheckAlignment_PSI_Gene.R R/Script_PLATE_05_PREPROCESS_3_4_CheckAlignment_SJ.R R/Script_PLATE_05_PREPROCESS_4_TransformGeneValues.R R/Script_PLATE_06_EVENTS_EXPRESSED.R R/Script_PLATE_07_MODALITY_ANALYSIS_1_AssignModality.R R/Script_PLATE_07_MODALITY_ANALYSIS_2_0_PropModality.R R/Script_PLATE_07_MODALITY_ANALYSIS_2_1_PropModality_Doughnut.R R/Script_PLATE_07_MODALITY_ANALYSIS_2_2_PropModality_Bar.R R/Script_PLATE_08_PCA_0_RunPCA.R R/Script_PLATE_08_PCA_1_RunPCA_PSI.R R/Script_PLATE_08_PCA_2_RunPCA_Gene.R R/Script_PLATE_08_PCA_4_RunPCA_PSI_Gene.R R/Script_PLATE_08_PCA_5_ComputeHighlyVariable_PSI.R R/Script_PLATE_09_DE_1_0_CompareValues.R R/Script_PLATE_09_DE_1_2_CompareValues_PSI.R R/Script_PLATE_09_DE_1_3_CompareValues_Gene.R R/Script_PLATE_09_DE_1_4_CompareValues_SplicedGene.R R/Script_PLATE_09_DE_1_5_SubsetCrypticA3SS.R R/Script_PLATE_09_DE_2_0_PlotDEValues.R R/Script_PLATE_09_DE_2_1_PlotDEValues_PSI_Distance.R R/Script_PLATE_09_DE_2_2_PlotDEValues_PSI_Mean.R R/Script_PLATE_09_DE_2_3_PlotDEValues_PSI_Mean_Group1vs2.R R/Script_PLATE_09_DE_2_4_PlotDEValues_Gene_Mean_Global.R R/Script_PLATE_09_DE_2_5_PlotDEValues_Gene_Mean_Spliced.R R/Script_PLATE_09_DE_3_PctASE.R R/Script_PLATE_09_DE_4_ModalityChange.R R/Script_PLATE_09_DE_5_1_IsoSwitch.R R/Script_PLATE_09_DE_5_2_IsoSwitch_PlotExpr.R R/Script_PLATE_09_DE_6_1_GO.R R/Script_PLATE_09_DE_6_2_GO_Plot.R R/Script_PLATE_10_PREDICT_NMD_1_ParseGTF.R R/Script_PLATE_10_PREDICT_NMD_2_0_FindPTC.R R/Script_PLATE_10_PREDICT_NMD_2_1_FindPTC_SE_PosStrand.R R/Script_PLATE_10_PREDICT_NMD_2_2_FindPTC_SE_NegStrand.R R/Script_PLATE_10_PREDICT_NMD_3_1_FindPTC_RI_PosStrand.R R/Script_PLATE_10_PREDICT_NMD_3_2_FindPTC_RI_NegStrand.R R/Script_PLATE_10_PREDICT_NMD_4_1_FindPTC_A5SS_PosStrand.R R/Script_PLATE_10_PREDICT_NMD_4_2_FindPTC_A5SS_NegStrand.R R/Script_PLATE_10_PREDICT_NMD_5_1_FindPTC_A3SS_PosStrand.R R/Script_PLATE_10_PREDICT_NMD_5_2_FindPTC_A3SS_NegStrand.R R/Script_PLATE_10_PREDICT_NMD_6_PropPTC.R R/Script_PLATE_10_PREDICT_NMD_7_CompareExpr.R R/Script_PLATE_10_PREDICT_NMD_8_AnnoVolcanoPlot.R R/Script_PLATE_11_ADHOC_PLOT_0_PlotValues.R R/Script_PLATE_11_ADHOC_PLOT_1_PlotValues_PSI.R R/Script_PLATE_11_ADHOC_PLOT_2_PlotValues_Gene.R README.md inst/doc/MARVEL.R inst/doc/MARVEL.Rmd man/AnnoVolcanoPlot.Rd man/AnnotateGenes.10x.Rd man/AnnotateSJ.10x.Rd man/AssignModality.Rd man/BioPathways.10x.Rd man/BioPathways.Plot.10x.Rd man/BioPathways.Plot.Rd man/BioPathways.Rd man/CheckAlignment.10x.Rd man/CheckAlignment.Exp.Rd man/CheckAlignment.PSI.Exp.Rd man/CheckAlignment.PSI.Rd man/CheckAlignment.Rd man/CheckAlignment.SJ.Rd man/CompareExpr.Rd man/CompareValues.Exp.Rd man/CompareValues.Exp.Spliced.Rd man/CompareValues.Genes.10x.Rd man/CompareValues.PSI.Rd man/CompareValues.Rd man/CompareValues.SJ.10x.Rd man/CompareValues.SJ.DonorLevel.10x.Rd man/ComputePSI.A3SS.Rd man/ComputePSI.A5SS.Rd man/ComputePSI.AFE.Rd man/ComputePSI.ALE.Rd man/ComputePSI.MXE.Rd man/ComputePSI.Posterior.Rd man/ComputePSI.RI.Rd man/ComputePSI.Rd man/ComputePSI.SE.Rd man/CountEvents.Rd man/CreateMarvelObject.10x.Rd man/CreateMarvelObject.Rd man/DetectEvents.AFE.NegStrand.Rd man/DetectEvents.AFE.PosStrand.Rd man/DetectEvents.AFE.Rd man/DetectEvents.ALE.NegStrand.Rd man/DetectEvents.ALE.PosStrand.Rd man/DetectEvents.ALE.Rd man/DetectEvents.Rd man/FilterGenes.10x.Rd man/FindPTC.A3SS.NegStrand.Rd man/FindPTC.A3SS.PosStrand.Rd man/FindPTC.A5SS.NegStrand.Rd man/FindPTC.A5SS.PosStrand.Rd man/FindPTC.RI.NegStrand.Rd man/FindPTC.RI.PosStrand.Rd man/FindPTC.Rd man/FindPTC.SE.NegStrand.Rd man/FindPTC.SE.PosStrand.Rd man/IdentifyVariableEvents.Rd man/IsoSwitch.10x.Rd man/IsoSwitch.PlotExpr.Rd man/IsoSwitch.Rd man/ModalityChange.Rd man/ParseGTF.Rd man/PctASE.Rd man/PlotDEValues.Exp.Global.Rd man/PlotDEValues.Exp.Spliced.Rd man/PlotDEValues.Genes.10x.Rd man/PlotDEValues.PSI.Distance.Rd man/PlotDEValues.PSI.Mean.Rd man/PlotDEValues.PSI.Mean.g2vsg1.Rd man/PlotDEValues.Rd man/PlotDEValues.SJ.10x.Rd man/PlotPctExprCells.Genes.10x.Rd man/PlotPctExprCells.SJ.10x.Rd man/PlotValues.Exp.Rd man/PlotValues.Gene.Pseudobulk.10x.Rd man/PlotValues.Gene.SingleCell.10x.Rd man/PlotValues.PCA.CellGroup.10x.Rd man/PlotValues.PCA.Gene.10x.Rd man/PlotValues.PCA.PSI.10x.Rd man/PlotValues.PSI.Pseudobulk.10x.Rd man/PlotValues.PSI.Pseudobulk.Heatmap.10x.Rd man/PlotValues.PSI.Rd man/PlotValues.Rd man/PrepareBedFile.RI.Rd man/Preprocess_rMATS.A3SS.Rd man/Preprocess_rMATS.A5SS.Rd man/Preprocess_rMATS.MXE.Rd man/Preprocess_rMATS.RI.Rd man/Preprocess_rMATS.Rd man/Preprocess_rMATS.SE.Rd man/PropModality.Bar.Rd man/PropModality.Doughnut.Rd man/PropModality.Rd man/PropPTC.Rd man/RemoveCrypticSS.AFE.Rd man/RemoveCrypticSS.ALE.Rd man/RemoveCrypticSS.Rd man/RunPCA.Exp.Rd man/RunPCA.PSI.Exp.Rd man/RunPCA.PSI.Rd man/RunPCA.Rd man/SubsetCrypticA3SS.Rd man/SubsetCrypticSS.A3SS.Rd man/SubsetCrypticSS.A5SS.Rd man/SubsetCrypticSS.Rd man/SubsetSamples.Rd man/TransformExpValues.Rd man/ValidateSJ.10x.Rd man/adhocGene.DE.Gene.10x.Rd man/adhocGene.DE.PSI.10x.Rd man/adhocGene.PlotDEValues.10x.Rd man/adhocGene.PlotSJPosition.10x.Rd man/adhocGene.TabulateExpression.Gene.10x.Rd man/adhocGene.TabulateExpression.PSI.10x.Rd vignettes/MARVEL.Rmd