MetaCell

Metacells — small, transcriptionally homogeneous groups of single cells used as the unit of analysis. Three layers: a recommended single-sample workflow, a multi-sample (batch-corrected) workflow, and a backend zoo comparing all seven ov.single.MetaCell partitioners.

• MetaCell
• Recommended workflow: SEACells end-to-end + downstream sanity
• Multi-sample metacells with batch correction

Backend zoo

• MetaCell zoo
• SEACells — kernel archetypal analysis
• MetaQ — VQ-VAE codebook metacells
• SuperCell — kNN graph + walktrap community detection
• k-means — the trivial baseline that’s often hard to beat
• random — the honest lower-bound baseline
• GeoSketch — density-aware sketching as a metacell baseline
• Side-by-side comparison of all metacell backends