Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

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Documentation for package ‘M3Drop’ version 1.18.0

Help Pages

bg__add_model_to_plot Make M3Drop Plots
bg__calc_variables Calculate Gene Variables
bg__default_mean2disp Mean to Dispersion
bg__dropout_plot_base Make M3Drop Plots
bg__expression_heatmap Plot Heatmap of Gene Expression
bg__filter_cells Filter Expression Data
bg__fitdispersion Perform Traditional Differential Expression
bg__fit_gamma Fit Gamma Distribution
bg__fit_logistic Fit functions to the dropouts vs expression distribution.
bg__fit_MM Fit functions to the dropouts vs expression distribution.
bg__fit_size_to_var Fit gene-specific dispersion
bg__fit_ZIFA Fit functions to the dropouts vs expression distribution.
bg__get_extreme_residuals Get outliers from MM curve.
bg__get_mean2disp Perform Traditional Differential Expression
bg__get_stats Calculate Simulation Statistics
bg__highlight_genes Make M3Drop Plots
bg__horizontal_residuals_MM_log10 Calculate Horizontal Residuals
bg__m3dropTraditionalDE Perform Traditional Differential Expression
bg__m3dropTraditionalDEShiftDisp Perform Traditional Differential Expression
bg__MakeSimData Make Simulated Data
bg__MakeSimDE Make Simulated Data
bg__MakeSimDVar Make Simulated Data
bg__MakeSimHVar Make Simulated Data
bg__nbumiGroupDE Perform Traditional Differential Expression
bg__shift_size Shift Size Parameter
bg__test_DE_K_equiv Differentially Expressed Genes.
bg__var_vs_drop Variance vs Dropout Rate
BrenneckeGetVariableGenes Identify Highly Variable Genes
Consensus_FS Consensus Feature Selection
corFS Other Feature Selection Methods
giniFS Other Feature Selection Methods
irlbaPcaFS Other Feature Selection Methods
M3DropCleanData Filter Expression Data
M3DropConvertData Convert Data to be suitable for M3Drop
M3DropDropoutModels Fit functions to the dropouts vs expression distribution.
M3DropExpressionHeatmap Plot Heatmap of Gene Expression
M3DropFeatureSelection Differentially Expressed Genes.
M3DropGetExtremes Get outliers from MM curve.
M3DropGetHeatmapClusters Extracts clusters/ordered names from heatmap output
M3DropGetHeatmapNames Extracts clusters/ordered names from heatmap output
M3DropGetMarkers Identify marker genes
M3DropSimulationTrifecta Make Simulated Data from a provided scRNASeq dataset.
M3DropTestShift Test for horizontal shift.
M3DropThreeSetVenn Three-way Venn Diagram
NBumiCheckFit Check Fit Quality
NBumiCheckFitFS Check Fit Quality
NBumiCoexpression Variance-based Feature Selection
NBumiCompareModels Compare negative binomial models
NBumiConvertData Convert Data to be suitable for NBumi
NBumiConvertToInteger Turn a matrix of expression values into integer counts
NBumiFeatureSelectionCombinedDrop Dropout-based Feature Selection
NBumiFeatureSelectionHighVar Variance-based Feature Selection
NBumiFitBasicModel Fit Depth-Adjusted Negative Binomial Model
NBumiFitDispVsMean Fit function between mean and dispersion
NBumiFitModel Fit Depth-Adjusted Negative Binomial Model
NBumiHVG Variance-based Feature Selection Accounting for Library Size and Sample Variance
NBumiImputeNorm Normalized Data using the DANB model
NBumiSimulationTrifecta Make Simulated Data from a provided scRNASeq dataset.
obsolete__nbumiFeatureSelectionDropouts Other Feature Selection Methods
obsolete__nbumiFeatureSelectionHighVarDist2Med Other Feature Selection Methods
PoissonUMIFeatureSelectionDropouts Dropout-based Feature Selection