bioalpha.singlecell.read_10x_h5

bioalpha.singlecell.read_10x_h5(filename: str | Path, genome: str | None = None, gex_only: bool = True, backup_url: str | None = None) → AnnData

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’

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

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