aggregateNonCountSignal	aggregateNonCountSignal
aggregateToPseudoBulk	aggregateToPseudoBulk
aggregateVar	aggregateVar
as.dreamletResult	as.dreamletResult
assay,dreamletProcessedData,ANY-method	assay-methods
assay,dreamletProcessedData,dreamletProcessedData-method	assay-methods
assay,dreamletResult,ANY-method	assay-methods
assay,dreamletResult,dreamletResult-method	assay-methods
assay,vpDF,ANY-method	assay-methods
assay,vpDF,vpDF-method	assay-methods
assayNames,dreamletProcessedData,dreamletProcessedData-method	assayNames-methods
assayNames,dreamletProcessedData-method	assayNames-methods
assayNames,dreamletResult,dreamletResult-method	assayNames-methods
assayNames,dreamletResult-method	assayNames-methods
assayNames,vpDF,vpDF-method	assayNames-methods
assayNames,vpDF-method	assayNames-methods
buildClusterTreeFromPB	buildClusterTreeFromPB
cellCounts	cellCounts
cellSpecificityValues-class	cellSpecificityValues-class
cellTypeSpecificity	cellTypeSpecificity
checkFormula	checkFormula
coefNames	coefNames-methods
coefNames,dreamletResult-method	coefNames-methods
colData,dreamletProcessedData-method	colData-dreamletProcessedData-method
colData<-,dreamletProcessedData,ANY-method	colData-set-dreamletProcessedData-ANY-method
compositePosteriorTest	compositePosteriorTest
computeCellCounts	computeCellCounts
computeLogCPM	computeLogCPM
computeNormCounts	computeNormCounts
details	details-methods
details,dreamletProcessedData-method	details-methods
details,dreamletResult-method	details-methods
details,vpDF-method	details-methods
diffVar,dreamletResult,dreamletResult-method	diffVar-methods
diffVar,dreamletResult-method	diffVar-methods
dreamlet	dreamlet
dreamlet,dreamletProcessedData-method	dreamlet
dreamletCompareClusters	dreamletCompareClusters
dreamletProcessedData-class	dreamletProcessedData-class
dreamletResult-class	dreamletResult-class
dreamlet_mash_result-class	dreamlet_mash_result-class
dropRedundantTerms	dropRedundantTerms
equalFormulas	equalFormulas
extractData	extractData-methods
extractData,dreamletProcessedData,character-method	extractData-methods
extractData,dreamletProcessedData-method	extractData-methods
fitVarPart	fitVarPart
fitVarPart,dreamletProcessedData-method	fitVarPart
getExprGeneNames	getExprGeneNames
getTreat,dreamletResult,dreamletResult-method	getTreat-methods
getTreat,dreamletResult-method	getTreat-methods
metadata,dreamletProcessedData,dreamletProcessedData-method	metadata-dreamletProcessedData-method
metadata,dreamletProcessedData-method	metadata-dreamletProcessedData-method
meta_analysis	meta_analysis
outlier	outlier
outlierByAssay	outlierByAssay
pbWeights	pbWeights
plotBeeswarm	plotBeeswarm
plotCellComposition	plotCellComposition
plotCellComposition,data.frame-method	plotCellComposition
plotCellComposition,matrix-method	plotCellComposition
plotCellComposition,SingleCellExperiment-method	plotCellComposition
plotForest	plotForest-methods
plotForest,dreamletResult-method	plotForest-methods
plotForest,dreamlet_mash_result-method	plotForest-methods
plotGeneHeatmap	plotGeneHeatmap-methods
plotGeneHeatmap,dreamletResult,dreamletResult-method	plotGeneHeatmap-methods
plotGeneHeatmap,dreamletResult-method	plotGeneHeatmap-methods
plotHeatmap	plotHeatmap-methods
plotHeatmap,cellSpecificityValues,cellSpecificityValues-method	plotHeatmap-methods
plotHeatmap,cellSpecificityValues-method	plotHeatmap-methods
plotHeatmap,data.frame,data.frame-method	plotHeatmap-methods
plotHeatmap,data.frame-method	plotHeatmap-methods
plotHeatmap,matrix,matrix-method	plotHeatmap-methods
plotHeatmap,matrix-method	plotHeatmap-methods
plotPCA	plotPCA
plotPCA,list-method	plotPCA
plotPercentBars,cellSpecificityValues,cellSpecificityValues-method	plotPercentBars-methods
plotPercentBars,cellSpecificityValues-method	plotPercentBars-methods
plotPercentBars,vpDF,vpDF-method	plotPercentBars-methods
plotPercentBars,vpDF-method	plotPercentBars-methods
plotProjection	plotProjection
plotVarPart,DataFrame,DataFrame-method	plotVarPart-methods
plotVarPart,DataFrame-method	plotVarPart-methods
plotViolin	plotViolin-methods
plotViolin,cellSpecificityValues,cellSpecificityValues-method	plotViolin-methods
plotViolin,cellSpecificityValues-method	plotViolin-methods
plotVolcano	plotVolcano-methods
plotVolcano,dreamlet_mash_result,dreamlet_mash_result-method	plotVolcano-methods
plotVolcano,dreamlet_mash_result-method	plotVolcano-methods
plotVolcano,list,list-method	plotVolcano-methods
plotVolcano,list-method	plotVolcano-methods
plotVolcano,MArrayLM,MArrayLM-method	plotVolcano-methods
plotVolcano,MArrayLM-method	plotVolcano-methods
plotVoom	plotVoom-methods
plotVoom,dreamletProcessedData,dreamletProcessedData-method	plotVoom-methods
plotVoom,dreamletProcessedData-method	plotVoom-methods
plotVoom,EList-method	plotVoom-methods
plotVoom,list,list-method	plotVoom-methods
print,dreamletProcessedData,dreamletProcessedData-method	print-methods
print,dreamletProcessedData-method	print-methods
print,dreamletResult,dreamletResult-method	print-methods
print,dreamletResult-method	print-methods
processAssays	processAssays
processOneAssay	processOneAssay
removeConstantTerms	removeConstantTerms
residuals,dreamletResult,dreamletResult-method	residuals-methods
residuals,dreamletResult-method	residuals-methods
run_mash	run_mash
seeErrors	seeErrors-methods
seeErrors,dreamletProcessedData-method	seeErrors-methods
seeErrors,dreamletResult-method	seeErrors-methods
seeErrors,vpDF-method	seeErrors-methods
show,dreamletProcessedData,dreamletProcessedData-method	show-methods
show,dreamletProcessedData-method	show-methods
show,dreamletResult,dreamletResult-method	show-methods
show,dreamletResult-method	show-methods
sortCols,vpDF-method	sortCols-method
stackAssays	stackAssays
tabToMatrix	tabToMatrix
topTable,dreamletResult,dreamletResult-method	topTable-methods
topTable,dreamletResult-method	topTable-methods
vpDF-class	vpDF-class
zenith_gsa,dreamletResult,GeneSetCollection,ANY-method	zenith_gsa-methods
zenith_gsa,dreamletResult,GeneSetCollection-method	zenith_gsa-methods
zenith_gsa,dreamlet_mash_result,GeneSetCollection,ANY-method	zenith_gsa-methods
zenith_gsa,dreamlet_mash_result,GeneSetCollection-method	zenith_gsa-methods
[,dreamletProcessedData,ANY,ANY,ANY-method	extract-methods
[,dreamletProcessedData,dreamletProcessedData-method	extract-methods
[,dreamletResult,ANY,ANY,ANY-method	extract-methods
[,dreamletResult,dreamletResult-method	extract-methods
