Single-cell Analysis / R package
muscat
Test expression differences within annotated cell populations across samples, including pseudobulk analysis.
Best fit
Analysts comparing conditions while treating samples or donors as the units of replication.
What you need
R and Bioconductor, counts, sample identifiers, cell labels, and an appropriate study design.
What to check
Rare cell populations may have too little sample coverage. More cells cannot replace missing biological replicates.