Package index • lucida

Analysis functions

lucida(): Negative Binomial Differential Expression Analysis
fitVarPart(): Variance Partitioning Analysis
findHVGs(): Find Highly Variable Genes
topHVGs(): Get Residuals For Highly Variable Genes
residuals(<lucida>): Residuals From Lucida Fit

Extract results

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

Plotting functions

plotDispEsts(<lucida>): Plot Dispersion Versus Mean Depth
plotExpression(): Plot expression
plotForest(): Plot forest
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

sortCols(): Sort Variance Partitioning Fractions
simulateCountData(): Simulate count data