biocontext_kb.core.panglaodb

biocontext_kb.core.panglaodb#

Functions#

get_panglaodb_marker_genes(species[, min_sensitivity, ...])

Retrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol.

get_panglaodb_options()

Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types.

Package Contents#

biocontext_kb.core.panglaodb.get_panglaodb_marker_genes(species, min_sensitivity=None, min_specificity=None, organ=None, cell_type=None, gene_symbol=None)#

Retrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol.

Returns:

Markers array with gene symbols, cell types, organs, sensitivity/specificity scores or error message.

Return type:

dict

Parameters:

  • species (Annotated[str, Field(description="Species: 'Hs' for Human or 'Mm' for Mouse")])

  • min_sensitivity (Annotated[Optional[float], Field(description='Minimum sensitivity score (0-1), applied to species-specific column', ge=0, le=1)])

  • min_specificity (Annotated[Optional[float], Field(description='Minimum specificity score (0-1), applied to species-specific column', ge=0, le=1)])

  • organ (Annotated[Optional[str], Field(description="Organ filter (e.g., 'Brain', 'Lung'), case-insensitive")])

  • cell_type (Annotated[Optional[str], Field(description="Cell type filter (e.g., 'Smooth muscle cells', 'T cells'), case-insensitive")])

  • gene_symbol (Annotated[Optional[str], Field(description="Gene symbol filter (e.g., 'MAFB', 'SYNPO'), case-insensitive")])

biocontext_kb.core.panglaodb.get_panglaodb_options()#

Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types.

Returns:

Lists of unique organ and cell_type values available in PanglaoDB dataset or error message.

Return type:

dict

Contents