Version Compatibility

Reference examples tested with: squidpy 1.4+, scanpy 1.10+, anndata 0.10+, commot 0.0.3+

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

• Python: pip show <package> then help(module.function) to check signatures

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

COMMOT is the distance-aware alternative shown below; LIANA+ wraps and benchmarks several methods/databases; CellChat v2 (R) and NicheNet (R) are noted in the decision table but not coded here.

Spatial Cell-Cell Communication

"Map cell-cell communication in my spatial data" -> Score ligand mRNA in a sender population against receptor mRNA in a receiver population, optionally weighted by spatial proximity, against a permutation null.

• Python: squidpy.gr.ligrec (CellPhoneDB engine, space-blind) or commot.tl.spatial_communication (optimal transport, distance-aware)
• R: CellChat v2 spatial mode, or NicheNet for downstream receiver-response linkage

Governing Principle