Metabolism

Tutorials for single-cell metabolism inference via ov.single.Metabolism, which dispatches to three complementary backends, plus ov.single.MetaboliteCCC for metabolite-mediated cell-cell communication:

• scMetabolism (method='scmetabolism') — metabolic pathway-activity scoring over curated KEGG / REACTOME gene sets (AUCell / VISION / ssGSEA / GSVA).

• scFEA (method='scfea') — a graph-neural-network estimate of flux through ~168 metabolic modules.

• Compass (method='compass') — constraint-based genome-scale reaction flux (loaded from a precomputed Compass run).

• MEBOCOST (ov.single.MetaboliteCCC) — metabolite cell-cell communication, reusing the ov.pl.ccc_* plots.

The per-cell backends write a unified schema (adata.obsm['X_metabolism'], adata.uns['metabolism']) so ov.pl.metabolism_heatmap works with any of them.

• Single-cell metabolic landscape of a head & neck tumour
• Metabolite cell-cell communication in a tumour microenvironment