from ._clone import *
from ._gene import *
from ._map import *
from ._utils import *

__all__ = [
    # _clone
    "clonal_fate_bias",
    "identify_persistent_clones",
    "fate_biased_clones",
    "coarse_grain_clone_over_cell_clusters",
    "get_normalized_coarse_X_clone",
    "clonal_trajectory",
    "add_clone_id_for_each_cell",
    "remove_multiclone_cell",
    "filter_cells",
    "remove_multicell_clone",
    "filter_clones",
    "clone_statistics",
    "get_distance_within_each_clone",
    "compute_sister_cell_distance",
    "generate_adata_from_X_clone",
    "conditional_heatmap",
    # _gene
    "differential_genes",
    "identify_TF_and_surface_marker",
    # _map
    "fate_hierarchy",
    "fate_coupling",
    "pvalue_for_fate_coupling",
    "fate_map",
    "fate_potency",
    "fate_bias",
    "progenitor",
    "iterative_differentiation",
    # _utils
    "get_normalized_covariance",
    "convert_to_tree",
    "compute_fate_probability_map",
    "mapout_trajectories",
    "compute_state_potential",
]
