Package index • lucida

Analysis functions

fitVarPart(): Variance Partitioning Analysis
findHVGs(): Find Highly Variable Genes
lucida(): Differential Expression Analysis
vst(): Variance Stabilizing Transform

Extract results

results(): Table of Results From Differential Expression Analysis
coef(<lucida>): Extract Model Coefficients

Plotting functions

plotDispEsts(<lucida>): Plot Dispersion Versus Mean Depth
plotMA(<lucida>): MA Plot of LogFC Versus Mean Expression
plotPercentBars(): Bar Plot of Variance Fractions
plotVarPart(): Violin Plot of Variance Fractions
plotVolcano(): Volcano Plot of Differential Expression Analysis
plotTrendVP(): Plot Trend of Variance Fractions Vs Count Magnitude

Other functions

coefNames(): Coefficient names
readH5AD(): Read H5AD as SingleCellExperiment
sortCols(): Sort Variance Partitioning Fractions
simulateCountData(): Simulate count data