Replication
Original thought was that multiple cells provided replication
However, this is still an n = 1 and biological replicates are required to get valid p.values
Pseudobulking within a sample is reported to outperform single cell DE methods
Single cell DE methods are reported to have a bias towards highly expressed genes even when their expression remains unchanged
Squair, J.W., Gautier, M., Kathe, C. et al. Confronting false discoveries in single-cell differential expression. Nat Commun 12, 5692 (2021)
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https://www.monash.edu/researchinfrastructure/mgbp