Man pages for tallulandrews/M3D
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
| 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_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 |
