Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

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Documentation for package ‘M3Drop’ version 1.35.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
NBumiPearsonResiduals	Calculate Pearson Residuals
NBumiPearsonResidualsApprox	Calculate Pearson Residuals
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