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

---

Documentation for package ‘muscat’ version 1.20.0

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

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
calcExprFreqs	calcExprFreqs
data	Example datasets
example_sce	Example datasets
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