# Multi-sample multi-group scRNA-seq data analysis tools

## Documentation for package ‘muscat’ version 1.25.4

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

## Help Pages

.mm_dream | DS analysis using mixed-models (MM)
.mm_dream2 | DS analysis using mixed-models (MM)
.mm_glmm | DS analysis using mixed-models (MM)
.mm_vst | DS analysis using mixed-models (MM)
aggregateData | Aggregation of single-cell to pseudobulk data
bbhw | bbhw: Bulk-based hypothesis weighing
calcExprFreqs | calcExprFreqs
data | Example datasets
example_sce | Example datasets
gBH | gBH - Grouped Benjamini-Hochberg procedure
mmDS | DS analysis using mixed-models (MM)
pbDD | pseudobulk DS analysis
pbDS | pseudobulk DS analysis
pbFlatten | pbFlatten Flatten pseudobulk SCE
pbHeatmap | Heatmap of cluster-sample pseudobulks
pbMDS | Pseudobulk-level MDS plot
prepSCE | Prepare SCE for DS analysis
prepSim | SCE preparation for 'simData'
resDS | resDS Formatting of DS analysis results
simData | simData
stagewise_DS_DD | Perform two-stage testing on DS and DD analysis results