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