from ._help_functions_CoSpar import *
from .tree_utils import Tree

__all__ = [
    "get_dge_SW",
    "sparse_var",
    "mean_center",
    "normalize_variance",
    "sparse_zscore",
    "corr2_coeff",
    "sparse_rowwise_multiply",
    "sparse_column_multiply",
    "matrix_row_or_column_thresholding",
    "get_pca",
    "runningquantile",
    "get_vscores",
    "filter_genes",
    "remove_corr_genes",
    "converting_id_from_fullSpace_to_subSpace",
    "converting_id_from_subSpace_to_fullSpace",
    "analyze_selected_fates",
    "compute_shortest_path_distance",
    "add_neighboring_cells_to_a_map",
    "get_hierch_order",
    "above_the_line",
    "save_map",
    "smooth_a_vector",
    "update_time_ordering",
    "check_adata_structure",
    "save_preprocessed_adata",
    "load_saved_adata_with_key",
    "check_available_map",
    "switch_adata_representation",
    "selecting_cells_by_time_points",
    "check_available_clonal_info",
    "check_available_choices",
    "compute_pca",
    "compute_default_cost_matrix",
    "compute_gene_exp_distance",
    "update_data_description",
    "set_up_folders",
    "get_X_clone_with_reference_ordering",
    "parse_output_choices",
    "rename_list",
    "check_input_parameters",
    "Tree",
]
