Man pages for GabrielHoffman/dreamlet
Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
| 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-methods | Get assay |
| assayNames-methods | 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-methods | Get coefficient names |
| colData-dreamletProcessedData-method | Extract colData from 'dreamletProcessedData' |
| colData-set-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-methods | Extract details from dreamletProcessedData |
| diffVar-methods | Test differential variance |
| dreamlet | Differential expression for each assay |
| dreamletCompareClusters | Differential expression between pair of assays |
| dreamlet_mash_result-class | Class dreamlet_mash_result |
| dreamletProcessedData-class | Class dreamletProcessedData |
| dreamletResult-class | Class dreamletResult |
| dropRedundantTerms | Drop redundant terms from the model |
| equalFormulas | Check if two formulas are equal |
| extractData-methods | Extract normalized expression and 'colData' |
| extract-methods | Subset with brackets |
| fitVarPart | Variance Partition analysis for each assay |
| getExprGeneNames | Get list of expressed genes for each assay |
| getTreat-methods | 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-methods | Forest plot |
| plotGeneHeatmap-methods | Heatmap of genes and assays |
| plotHeatmap-methods | Plot heatmap |
| plotPCA | Plot PCA of gene expression for an assay |
| plotPercentBars-methods | Bar plot of variance fractions |
| plotProjection | Plot 2D projection |
| plotVarPart-methods | Violin plot of variance fractions |
| plotViolin-methods | Plot Violins |
| plotVolcano-methods | Volcano plot for each cell type |
| plotVoom-methods | Plot voom curves from each cell type |
| print-methods | Print object |
| processAssays | Processing SingleCellExperiment to dreamletProcessedData |
| processOneAssay | Processing expression data from assay |
| removeConstantTerms | Remove constant terms from formula |
| residuals-methods | Extract residuals from 'dreamletResult' |
| run_mash | Run mash analysis on dreamlet results |
| seeErrors-methods | Get error text |
| show-methods | Show object |
| sortCols-method | Sort variance partition statistics |
| stackAssays | Stack assays from pseudobulk |
| tabToMatrix | Convert results table to matrix |
| topTable-methods | Table of Top Genes from dreamlet fit |
| vpDF-class | Class vpDF |
| zenith_gsa-methods | Perform gene set analysis using zenith |
