monkeybread.calc.cell_transcript_proximity

monkeybread.calc.cell_transcript_proximity(adata, cells, genes=None)

Detects transcripts in proximity or inside a given list of cells.

Parameters

• adata (AnnData) – Annotated data matrix.

• cells (List[str]) – A list of cell ids to determine proximity.

• genes (Optional[List[str]] (default: None)) – An optional list of genes to filter. If not provided, all transcripts will be included.

Return type

DataFrame

Returns

Transcripts in proximity to the list of cells provided, with a column for gene, x, and y.