xchrom.readfile.read_10x_h5_to_h5ad

xchrom.readfile.read_10x_h5_to_h5ad(h5_file: str | Path, output_file: str | Path, genome: str | None = None, paired: bool = False) → AnnData[source]

Read 10x Genomics h5 file and convert to h5ad format

Parameters:

  • h5_file – Path to 10x Genomics h5 file

  • output_file – Output h5ad file path

  • genome – Name of the genome. If None, uses the first available genome

  • paired – Whether input paired RNA and ATAC adata objects, default False

Returns:

Converted AnnData object

Return type:

anndata.AnnData