Version Compatibility

Reference examples tested with: scanpy 1.10+, Seurat 5.0+, scvi-tools 1.1+, harmonypy 0.0.10+

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.

Batch Integration

"Integrate my batches" -> Learn a shared low-dimensional representation that mixes technical batches while preserving biological cell states, then cluster and visualize on it.

• Python: sce.pp.harmony_integrate, scvi.model.SCVI, sce.pp.bbknn, scanorama
• R: RunHarmony, IntegrateLayers (Seurat v5), fastMNN (batchelor)

Governing Principle