Version Compatibility

Reference examples tested with: scanpy 1.10+, Seurat 5.0+, celltypist 1.6+

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.

Automated Reference-Based Cell Annotation

"Annotate my cells from a reference" -> Transfer labels from an annotated reference or pretrained model onto query cells, with a calibrated confidence/rejection step.

• Python: celltypist.annotate() (pretrained LR) or scvi-tools scANVI label transfer
• R: SingleR() (correlation to a reference) or RunAzimuth() (anchor-based mapping)

Governing principle