scanpy.queries.biomart_annotations

scanpy.queries.biomart_annotations(org, attrs, *, host='www.ensembl.org', use_cache=False)

Retrieve gene annotations from ensembl biomart.

Parameters

org : str

Organism to query. Must be an organism in ensembl biomart. “hsapiens”, “mmusculus”, “drerio”, etc.

attrs : Iterable[str]

Attributes to query biomart for.

host : str (default: 'www.ensembl.org')

A valid BioMart host URL. Alternative values include archive urls (like “grch37.ensembl.org”) or regional mirrors (like “useast.ensembl.org”).

use_cache : bool (default: False)

Whether pybiomart should use a cache for requests. Will create a .pybiomart.sqlite file in current directory if used.

Return type

DataFrame

Returns

Dataframe containing annotations.

Examples

Retrieve genes coordinates and chromosomes

>>> import scanpy as sc
>>> annot = sc.queries.biomart_annotations(
        "hsapiens",
        ["ensembl_gene_id", "start_position", "end_position", "chromosome_name"],
    ).set_index("ensembl_gene_id")
>>> adata.var[annot.columns] = annot