Version Compatibility

Reference examples tested with: scanpy 1.10+, Seurat 5.0+, anndata 0.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Marker Gene Detection and Manual Annotation

"Find marker genes for my clusters" -> Rank genes that separate each cluster from the rest, then map clusters to cell types using canonical markers.

• Python: sc.tl.rank_genes_groups() -> filter by effect size + fraction expressing -> adata.obs[...].map(labels)
• R: Seurat::FindAllMarkers() -> filter by avg_log2FC + pct.1/pct.2 -> RenameIdents()

Governing principle