[,dreamletResult,ANY,ANY,ANY-method
                        Subset with brackets
aggregateNonCountSignal
                        Aggregation of single-cell signals
aggregateToPseudoBulk   Aggregation of single-cell to pseudobulk data
aggregateVar            Per-sample variance of single-cell counts
as.dreamletResult       Convert list of regression fits to
                        'dreamletResult'
assay,dreamletResult,ANY-method
                        Get assay
assayNames,dreamletResult-method
                        Get assayNames
buildClusterTreeFromPB
                        Hierarchical clustering on cell types from
                        pseudobulk
cellCounts              Extract cell counts
cellSpecificityValues-class
                        Class cellSpecificityValues
cellTypeSpecificity     Get cell type specificity of gene expression
checkFormula            Check variables in a formula
coefNames               Get coefficient names
colData,dreamletProcessedData-method
                        Extract colData from 'dreamletProcessedData'
colData<-,dreamletProcessedData,ANY-method
                        Set colData
compositePosteriorTest
                        Perform composite test on results from mashr
computeCellCounts       Get cell counts with metadata
computeLogCPM           Compute log normalized counts
computeNormCounts       Compute normalized counts
details                 Extract details from dreamletProcessedData
diffVar,dreamletResult-method
                        Test differential variance
dreamlet                Differential expression for each assay
dreamletCompareClusters
                        Differential expression between pair of assays
dreamletProcessedData-class
                        Class dreamletProcessedData
dreamletResult-class    Class dreamletResult
dreamlet_mash_result-class
                        Class dreamlet_mash_result
dropRedundantTerms      Drop redundant terms from the model
equalFormulas           Check if two formulas are equal
extractData             Extract normalized expression and 'colData'
fitVarPart              Variance Partition analysis for each assay
getExprGeneNames        Get list of expressed genes for each assay
getTreat,dreamletResult-method
                        Test if coefficient is different from a
                        specified value
meta_analysis           Meta-analysis across multiple studies
metadata,dreamletProcessedData-method
                        Extract metadata from 'dreamletProcessedData'
outlier                 Multivariate outlier detection
outlierByAssay          Outlier analysis for each assay
pbWeights               Compute precision weights for pseudobulk
plotBeeswarm            Beeswarm plot of effect sizes for each assay
plotCellComposition     Bar plot of cell compositions
plotForest              Forest plot
plotGeneHeatmap         Heatmap of genes and assays
plotHeatmap             Plot heatmap
plotPCA                 Plot PCA of gene expression for an assay
plotPercentBars,vpDF-method
                        Bar plot of variance fractions
plotProjection          Plot 2D projection
plotVarPart,DataFrame-method
                        Violin plot of variance fractions
plotViolin              Plot Violins
plotVolcano             Volcano plot for each cell type
plotVoom                Plot voom curves from each cell type
print,dreamletResult-method
                        Print object
processAssays           Processing SingleCellExperiment to
                        dreamletProcessedData
processOneAssay         Processing expression data from assay
removeConstantTerms     Remove constant terms from formula
residuals,dreamletResult-method
                        Extract residuals from 'dreamletResult'
run_mash                Run mash analysis on dreamlet results
seeErrors               Get error text
show,dreamletResult-method
                        Show object
sortCols,vpDF-method    Sort variance partition statistics
stackAssays             Stack assays from pseudobulk
tabToMatrix             Convert results table to matrix
topTable,dreamletResult-method
                        Table of Top Genes from dreamlet fit
vpDF-class              Class vpDF
zenith_gsa,dreamletResult,GeneSetCollection-method
                        Perform gene set analysis using zenith
