hest.batch_effect.filter_hest_stromal_housekeeping

hest.batch_effect.filter_hest_stromal_housekeeping(meta_df: DataFrame, hest_dir, whole_tissue=False, unify_genes=False, verbose=False) → List[HESTData]

Filter the genes of HESTData samples, such that: - only stable housekeeping genes are kept (see assets/MostStable_{species}.csv). - only stromal regions are kept (determined from CellViT segmentation)

The lists of most stable housekeeping genes across organs were taken from https://housekeeping.unicamp.br/?download

Parameters:

  • meta_df (pd.DataFrame) – panda dataframe containing the following columns [‘id’, ‘species’]

  • whole_tissue (bool, optional) – whenever to only keep stromal regions. Defaults to False.

  • unify_genes (bool, optional) – whenever to all the gene names beforehand. Defaults to False.

Returns:

filtered list of sc.AnnData containing only stromal regions and stable housekeeping genes

Return type:

List[HESTData]