bg__fit_gamma | Fit Gamma Distribution |
bg__get_stats | Calculate Simulation Statistics |
bg__mean2disp | Mean to Dispersion |
bg__shift_size | Shift Size Parameter |
bg__var_vs_drop | Variance vs Dropout Rate |
Brennecke_getVariableGenes | Identify Highly Variable Genes |
Consensus_FS | Consensus Feature Selection |
Fitting_Dropout_Models | Fit functions to the dropouts vs expression distribution. |
Imputation | Normalized Data using the DANB model |
M3D_calc_var | Calculate Gene Variables |
M3D_Clean_Data | Filter Expression Data |
M3D_ConverData | Convert Data to be suitable for M3Drop |
M3D_Differential_Expression | Differentially Expressed Genes. |
M3D_Dropout_Models | Fit functions to the dropouts vs expression distribution. |
M3D_Expression_Heatmap | Plot Heatmap of Gene Expression |
M3D_Get_Extremes | Get outliers from MM curve. |
M3D_Get_Heatmap_Cell_Clusters | Extracts clusters/ordered names from heatmap output |
M3D_getmarkers | Identify marker genes |
M3D_horz_res | Calculate Horizontal Residuals |
M3D_Plotting | Make M3Drop Plots |
M3D_Simulations | Make Simulated Data |
M3D_Test_Shift | Test for horizontal shift. |
M3D_ThreeSet_Venn | Three-way Venn Diagram |
M3D_TraditionalDE | Perform Traditional Differential Expression |
NBumi_CheckFit | Check Fit Quality |
NBumi_CoExpression | Variance-based Feature Selection |
NBumi_CompareModels | Compare negative binomial models |
NBumi_ConvertToInteger | Turn a matrix of expression values into integer counts |
NBumi_ConvrtData | Convert Data to be suitable for NBumi |
NBumi_FitDisp | Fit gene-specific dispersion |
NBumi_FitDispVsMean | Fit function between mean and dispersion |
NBumi_FitModel | Fit Depth-Adjusted Negative Binomial Model |
NBumi_FSDrop | Dropout-based Feature Selection |
NBumi_FSHighVar | Variance-based Feature Selection |
NBumi_FSOther | Other Feature Selection Methods |
NBumi_HVG | Variance-based Feature Selection Accounting for Library Size... |
NBumi_PearsonResiduals | Calculate Pearson Residuals |
NBumi_TradDE | Perform Traditional Differential Expression |
NewSimulations | Make Simulated Data from a provided scRNASeq dataset. |
Other_FS | Other Feature Selection Methods |
PoissonUMIFeatureSelectionDropouts | Dropout-based Feature Selection |
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