# Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

## Documentation for package ‘dreamlet’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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-method | Get assay
assayNames-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
coefNames-method | Get coefficient names
colData-method | Extract colData from 'dreamletProcessedData'
colData<--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
details-method | Extract details from dreamletProcessedData
diffVar-method | Test differential variance
dreamlet | Differential expression for each assay
dreamlet-method | 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'
extractData-method | Extract normalized expression and 'colData'
fitVarPart | Variance Partition analysis for each assay
fitVarPart-method | Variance Partition analysis for each assay
getExprGeneNames | Get list of expressed genes for each assay
getTreat-method | Test if coefficient is different from a specified value
metadata-method | Extract metadata from 'dreamletProcessedData'
meta_analysis | Meta-analysis across multiple studies
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
plotCellComposition-method | Bar plot of cell compositions
plotForest | Forest plot
plotForest-method | Forest plot
plotGeneHeatmap | Heatmap of genes and assays
plotGeneHeatmap-method | Heatmap of genes and assays
plotHeatmap | Plot heatmap
plotHeatmap-method | Plot heatmap
plotPCA | Plot PCA of gene expression for an assay
plotPCA-method | Plot PCA of gene expression for an assay
plotPercentBars-method | Bar plot of variance fractions
plotProjection | Plot 2D projection
plotVarPart-method | Violin plot of variance fractions
plotViolin | Plot Violins
plotViolin-method | Plot Violins
plotVolcano | Volcano plot for each cell type
plotVolcano-method | Volcano plot for each cell type
plotVoom | Plot voom curves from each cell type
plotVoom-method | Plot voom curves from each cell type
print-method | Print object
processAssays | Processing SingleCellExperiment to dreamletProcessedData
processOneAssay | Processing expression data from assay
removeConstantTerms | Remove constant terms from formula
residuals-method | Extract residuals from 'dreamletResult'
run_mash | Run mash analysis on dreamlet results
seeErrors | Get error text
seeErrors-method | Get error text
show-method | Show object
sortCols-method | Sort variance partition statistics
stackAssays | Stack assays from pseudobulk
tabToMatrix | Convert results table to matrix
topTable-method | Table of Top Genes from dreamlet fit
vpDF-class | Class vpDF
zenith_gsa-method | Perform gene set analysis using zenith
[-method | Subset with brackets