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.

Single-Cell Clustering

"Cluster my cells" -> Build a k-nearest-neighbor graph in PCA space, partition it into communities, and embed in 2D for display.

• Python: sc.pp.neighbors + sc.tl.leiden + sc.tl.umap (Scanpy)
• R: FindNeighbors + FindClusters + RunUMAP (Seurat)

Governing Principle