scatrans.list_bundled_gene_sets#
- scatrans.list_bundled_gene_sets(verbose=False)[source]#
List gene set files (.gmt and similar) that are bundled inside the package under scatrans/data/.
These are typically ClusterProfiler-derived GO/KEGG sets that you can use for better consistency with clusterProfiler results (same gene-term mappings).
Users can pass the filename (with or without extension) to run_enrichment(gene_sets=…) or run_kegg(…).
Example
sets = scat.list_bundled_gene_sets() # Recommended: just use base names + organism (auto-resolves to the Hs/Mm 2026 built-ins) res = scat.run_kegg(genes, organism=”mouse”) res = scat.run_enrichment(genes, gene_sets=”GO_Biological_Process”, organism=”mouse”) # Legacy names are also accepted and mapped to the 2026 sets.