.getAllUniContrasts	dot-getAllUniContrasts
.isMixedModelFormula	dot-isMixedModelFormula
.standard_transform	dot-standard_transform
applyQualityWeights	applyQualityWeights
as.data.frame.varPartResults	as.data.frame.varPartResults
as.matrix	as.matrix-varPartResults-method
as.matrix,varPartResults-method	as.matrix-varPartResults-method
calcVarPart	calcVarPart-method
calcVarPart,glm-method	calcVarPart-method
calcVarPart,glmer-method	calcVarPart-method
calcVarPart,glmerMod-method	calcVarPart-method
calcVarPart,lm-method	calcVarPart-method
calcVarPart,lmerMod-method	calcVarPart-method
calcVarPart,negbin-method	calcVarPart-method
canCorPairs	canCorPairs
classifyTestsF	classifyTestsF
classifyTestsF,MArrayLM2-method	classifyTestsF-MArrayLM2-method
colinearityScore	colinearityScore
countMatrix	varPartDEdata
dream	dream-method
dscchisq	dscchisq
eBayes,MArrayLM2-method	eBayes-method
eBayesFMT	eBayesFMT
ESS	ESS-method
ESS,lmerMod-method	ESS-method
extractVarPart	extractVarPart
fitExtractVarPartModel	fitExtractVarPartModel-method
fitExtractVarPartModel,data.frame-method	fitExtractVarPartModel-method
fitExtractVarPartModel,EList-method	fitExtractVarPartModel-method
fitExtractVarPartModel,ExpressionSet-method	fitExtractVarPartModel-method
fitExtractVarPartModel,matrix-method	fitExtractVarPartModel-method
fitExtractVarPartModel,sparseMatrix-method	fitExtractVarPartModel-method
fitVarPartModel	fitVarPartModel-method
fitVarPartModel,data.frame-method	fitVarPartModel-method
fitVarPartModel,EList-method	fitVarPartModel-method
fitVarPartModel,ExpressionSet-method	fitVarPartModel-method
fitVarPartModel,matrix-method	fitVarPartModel-method
fitVarPartModel,sparseMatrix-method	fitVarPartModel-method
FMT	FMT
FMT-class	FMT-class
FMT.ZI	FMT.ZI
geneCounts	varPartData
geneExpr	varPartData
getContrast	getContrast-method
getTreat	getTreat-method
getTreat,MArrayLM-method	getTreat-method
getTreat,MArrayLM2-method	getTreat-method
get_prediction	get_prediction-method
get_prediction,lm-method	get_prediction-method
get_prediction,lmerMod-method	get_prediction-method
ggColorHue	ggColorHue
info	varPartData
isRunableFormula	isRunableFormula
makeContrastsDream	makeContrastsDream
MArrayLM2-class	MArrayLM2-class
metadata	varPartDEdata
plotCompareP	plotCompareP-method
plotContrasts	plotContrasts
plotCorrMatrix	plotCorrMatrix
plotCorrStructure	plotCorrStructure
plotPercentBars	plotPercentBars-method
plotPercentBars,data.frame-method	plotPercentBars-method
plotPercentBars,matrix-method	plotPercentBars-method
plotPercentBars,varPartResults-method	plotPercentBars-method
plotStratify	plotStratify
plotStratifyBy	plotStratifyBy
plotVarianceEstimates	plotVarianceEstimates
plotVarPart	plotVarPart-method
plotVarPart,data.frame-method	plotVarPart-method
plotVarPart,matrix-method	plotVarPart-method
plotVarPart,varPartResults-method	plotVarPart-method
rdf.merMod	rdf.merMod
rdf_from_matrices	rdf_from_matrices
reOnly	reOnly
residuals,MArrayLM-method	residuals-MArrayLM-method
residuals,MArrayLM2-method	residuals-MArrayLM2-method
residuals,VarParFitList-method	residuals-VarParFitList-method
residuals.MArrayLM2	residuals.MArrayLM2
shrinkageMetric	shrinkageMetric
sortCols	sortCols-method
sortCols,data.frame-method	sortCols-method
sortCols,matrix-method	sortCols-method
sortCols,varPartResults-method	sortCols-method
subset.MArrayLM2,MArrayLM2-method	subset.MArrayLM2-method
topTable	toptable-method
topTable,FMT-method	toptable-method
toptable,FMT-method	toptable-method
toptable,MArrayLM-method	toptable-method
topTable,MArrayLM2-method	toptable-method
toptable,MArrayLM2-method	toptable-method
VarParCIList-class	VarParCIList-class
VarParFitList-class	VarParFitList-class
varParFrac-class	varParFrac-class
varPartConfInf	varPartConfInf
varPartData	varPartData
varPartDEdata	varPartDEdata
varPartResults-class	varPartResults-class
voomWithDreamWeights	voomWithDreamWeights
[.MArrayLM2	subset.MArrayLM2-method
