simba.read_10x_h5

simba.read_10x_h5(filename, genome=None, gex_only=True)

Read 10x-Genomics-formatted hdf5 file.

Parameters:

• filename – Path to a 10x hdf5 file.

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

Returns:

adata – Annotated data matrix, where observations/cells are named by their barcode and variables/genes by gene name

Return type:

AnnData