Version Compatibility

Reference examples tested with: miloR 2.0+, scCODA 0.1.9+, sccomp 1.8+, speckle 1.0+

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.

Differential Abundance Testing

"Did cell-type proportions change between conditions?" -> Test whether populations expanded or contracted between groups, accounting for the fact that proportions are not independent.

• R (cluster-free): miloR - build kNN graph, define neighborhoods, testNhoods() with a GLM and SpatialFDR
• Python/R (cluster-based): scCODA (Bayesian Dirichlet-multinomial), sccomp (Bayesian, outlier-robust), propeller (speckle, arcsin-sqrt + limma)

Governing principle