from .utils import update_rep, X_from_rep, W_from_rep, knn_is_cached

from .data_aggregation import aggregate_matrices
from .preprocessing import (
    qc_metrics,
    get_filter_stats,
    filter_data,
    run_filter_data,
    log_norm,
    select_features,
    pca,
)
from .hvf_selection import estimate_feature_statistics, highly_variable_features
from .batch_correction import set_group_attribute, correct_batch
from .nearest_neighbors import (
    calculate_nearest_neighbors,
    get_neighbors,
    neighbors,
    calculate_affinity_matrix,
    calc_kBET,
    calc_kSIM,
)
from .graph_operations import construct_graph
from .diffusion_map import diffmap, reduce_diffmap_to_3d
from .pseudotime import calc_pseudotime, infer_path
from .clustering import louvain, leiden, spectral_louvain, spectral_leiden
from .net_regressor import net_train_and_predict
from .visualization import (
    tsne,
    fitsne,
    umap,
    fle,
    net_tsne,
    net_fitsne,
    net_umap,
    net_fle,
)
from .diff_expr import de_analysis, markers, write_results_to_excel, run_de_analysis
from .gradient_boosting import find_markers, run_find_markers
from .convert_to_parquet import convert_to_parquet, run_conversion
from .scp_output import (
    run_scp_output,
    scp_write_coords,
    scp_write_metadata,
    scp_write_expression,
)
from .down_sampling import down_sample
from .subcluster_utils import get_anndata_for_subclustering
