Version Compatibility

Reference examples tested with: squidpy 1.4+, scanpy 1.10+, anndata 0.10+, esda 2.5+, libpysal 4.9+ (SPARK, SPARK-X, and nnSVG are R/Bioconductor packages)

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.

Spatial Statistics

"Find spatially variable genes / run Moran's I / test which cell types colocalize" -> Quantify spatial structure in expression or in cell-type arrangement against an explicit null model.

• Python: squidpy.gr.spatial_autocorr (Moran/Geary), squidpy.gr.nhood_enrichment, squidpy.gr.co_occurrence, esda.Moran_Local/esda.getisord.G_Local (LISA, Getis-Ord)
• R: SPARK / SPARK-X / nnSVG (SVG), spdep (Moran/Geary/Getis-Ord/LISA)

Governing Principle