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 Path | str

Path to a 10x hdf5 file.

genome str | None (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 str | None (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 for a feature barcode matrix, probe names for a probe bc matrix

var['gene_ids']

Gene IDs

var['feature_types']

Feature types

obs[filtered_barcodes]

filtered barcodes if present in the matrix

var

Any additional metadata present in /matrix/features is read in.