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

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Documentation for package ‘dreamlet’ version 1.0.3

• 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