lamindb.examples.cellxgene¶
CELLxGENE utilities.
- lamindb.examples.cellxgene.save_cellxgene_defaults()¶
- Save default values of the CELLxGENE schema to the instance. - Adds CELLxGENE specific (control) values that are not available in the ontologies: :rtype: - None- “normal” Disease 
- “na” Ethnicity 
- “unknown” entries for DevelopmentalStage, Phenotype, and CellType 
- “tissue”, “organoid”, and “cell culture” ULabels (tissue_type) 
- “cell”, “nucleus”, “na” ULabels (suspension_type) 
 
- lamindb.examples.cellxgene.create_cellxgene_schema(schema_version, *, field_types='ontology_id', organism='human', spatial_library_id=None)¶
- Generates a - Schemafor a specific CELLxGENE schema version.- Parameters:
- schema_version ( - Literal[- '4.0.0',- '5.0.0',- '5.1.0',- '5.2.0',- '5.3.0',- '6.0.0']) – The CELLxGENE Schema version.
- field_types ( - Literal[- 'ontology_id',- 'name'] |- Collection[- Literal[- 'ontology_id',- 'name']], default:- 'ontology_id') – One or several of ‘ontology_id’, ‘name’.
- organism ( - Literal[- 'human',- 'mouse',- 'zebra danio',- 'rhesus macaquedomestic pig',- 'chimpanzee',- 'white-tufted-ear marmoset',- 'sars-2'], default:- 'human') – The organism of the Schema.
- library_id – Identifier for the spatial library. Specifying this value enables curation against spatial requirements. 
 
- Return type: