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

bg__fit_gammaFit Gamma Distribution
bg__get_statsCalculate Simulation Statistics
bg__mean2dispMean to Dispersion
bg__shift_sizeShift Size Parameter
bg__var_vs_dropVariance vs Dropout Rate
Brennecke_getVariableGenesIdentify Highly Variable Genes
Consensus_FSConsensus Feature Selection
Fitting_Dropout_ModelsFit functions to the dropouts vs expression distribution.
ImputationNormalized Data using the DANB model
M3D_calc_varCalculate Gene Variables
M3D_Clean_DataFilter Expression Data
M3D_ConverDataConvert Data to be suitable for M3Drop
M3D_Differential_ExpressionDifferentially Expressed Genes.
M3D_Dropout_ModelsFit functions to the dropouts vs expression distribution.
M3D_Expression_HeatmapPlot Heatmap of Gene Expression
M3D_Get_ExtremesGet outliers from MM curve.
M3D_Get_Heatmap_Cell_ClustersExtracts clusters/ordered names from heatmap output
M3D_getmarkersIdentify marker genes
M3D_horz_resCalculate Horizontal Residuals
M3D_PlottingMake M3Drop Plots
M3D_SimulationsMake Simulated Data
M3D_Test_ShiftTest for horizontal shift.
M3D_ThreeSet_VennThree-way Venn Diagram
M3D_TraditionalDEPerform Traditional Differential Expression
NBumi_CheckFitCheck Fit Quality
NBumi_CompareModelsCompare negative binomial models
NBumi_ConvertToIntegerTurn a matrix of expression values into integer counts
NBumi_ConvrtDataConvert Data to be suitable for NBumi
NBumi_FitDispFit gene-specific dispersion
NBumi_FitDispVsMeanFit function between mean and dispersion
NBumi_FitModelFit Depth-Adjusted Negative Binomial Model
NBumi_FSDropDropout-based Feature Selection
NBumi_FSHighVarVariance-based Feature Selection
NBumi_FSOtherOther Feature Selection Methods
NBumi_TradDEPerform Traditional Differential Expression
NewSimulationsMake Simulated Data from a provided scRNASeq dataset.
Other_FSOther Feature Selection Methods
PoissonUMIFeatureSelectionDropoutsDropout-based Feature Selection
tallulandrews/M3D documentation built on Dec. 17, 2018, 9:24 p.m.