ovrlpy.io.read_Xenium

ovrlpy.io.read_Xenium(filepath, *, min_qv=None, remove_features=XENIUM_CTRLS, additional_columns=[], n_threads=None)

Read a Xenium transcripts file.

Parameters:

  • filepath (PathLike or str) – Path to the Xenium transcripts file. Both, .csv.gz and .parquet files, are supported.

  • min_qv (float | None, optional) – Minimum Phred-scaled quality value (Q-Score) of a transcript to be included. If None no filtering is performed.

  • remove_features (Collection[str], optional) – List of regex patterns to filter the ‘feature_name’ column, ovrlpy.io.XENIUM_CTRLS by default.

  • additional_columns (Collection[str], optional) – Additional columns to load from the transcripts file.

  • n_threads (int | None, optional) – Number of threads used for parsing the input file. If None, will default to number of available CPUs.

Return type:

polars.DataFrame