scanpy.read_10x_h5

scanpy.read_10x_h5(filename, genome=None, gex_only=True, backup_url=None)

Read 10x-Genomics-formatted hdf5 file.

Parameters

filename : Union[str, Path]

Path to a 10x hdf5 file.

genome : Optional[str] (default: None)

Filter expression to genes within this genome. For legacy 10x h5 files, this must be provided if the data contains more than one genome.

gex_only : bool (default: True)

Only keep ‘Gene Expression’ data and ignore other feature types, e.g. ‘Antibody Capture’, ‘CRISPR Guide Capture’, or ‘Custom’

backup_url : Optional[str] (default: None)

Retrieve the file from an URL if not present on disk.

Return type

AnnData

Returns

Annotated data matrix, where observations/cells are named by their barcode and variables/genes by gene name. Stores the following information:

X

The data matrix is stored

obs_names

Cell names

var_names

Gene names

var['gene_ids']

Gene IDs

var['feature_types']

Feature types