.getAllUniContrasts     Get all univariate contrasts
.isMixedModelFormula    Check if model contains a random effect
.standard_transform     Compute standard post-processing values
ESS                     Effective sample size
MArrayLM2-class         Class MArrayLM2
VarParCIList-class      Class VarParCIList
VarParFitList-class     Class VarParFitList
[.MArrayLM2             Subseting for MArrayLM2
as.data.frame,varPartResults-method
                        Convert to data.frame
as.matrix,varPartResults-method
                        Convert to matrix
calcVarPart             Compute variance statistics
canCorPairs             canCorPairs
classifyTestsF          Multiple Testing Genewise Across Contrasts
classifyTestsF,MArrayLM2-method
                        Multiple Testing Genewise Across Contrasts
colinearityScore        Collinearity score
dream                   Differential expression with linear mixed model
eBayes,MArrayLM2-method
                        eBayes for MArrayLM2
extractVarPart          Extract variance statistics
fitExtractVarPartModel
                        Fit linear (mixed) model, report variance
                        fractions
fitVarPartModel         Fit linear (mixed) model
getContrast             Extract contrast matrix for linear mixed model
getVarianceComponents   Extract variance terms
ggColorHue              Default colors for ggplot
plotCompareP            Compare p-values from two analyses
plotContrasts           Plot representation of contrast matrix
plotCorrMatrix          plotCorrMatrix
plotCorrStructure       plotCorrStructure
plotPercentBars         Bar plot of variance fractions
plotStratify            plotStratify
plotStratifyBy          plotStratifyBy
plotVarPart             Violin plot of variance fractions
residuals,MArrayLM2-method
                        residuals for MArrayLM2
residuals,VarParFitList-method
                        Residuals from model fit
sortCols                Sort variance partition statistics
topTable,MArrayLM2-method
                        toptable for MArrayLMM_lmer
varParFrac-class        Class varParFrac
varPartConfInf          Linear mixed model confidence intervals
varPartDEdata           Simulation dataset for dream example
varPartData             Simulation dataset for examples
varPartResults-class    Class varPartResults
voomWithDreamWeights    Transform RNA-Seq Data Ready for Linear Mixed
                        Modelling with dream()
