from .utils import (
    eff_n_jobs,
    update_rep,
    X_from_rep,
    W_from_rep,
    to_csr_or_dense,
    slicing,
    calc_mean,
    calc_mean_and_var,
    calc_expm1,
    calc_stat_per_batch,
    calc_sig_background,
    simulate_doublets,
    check_batch_key,
    predefined_signatures,
    predefined_pathways,
    load_signatures_from_file,
    largest_variance_from_random_matrix,
)

from .preprocessing import (
    qc_metrics,
    get_filter_stats,
    filter_data,
    identify_robust_genes,
    _run_filter_data,
    log_norm,
    normalize,
    log1p,
    arcsinh,
    select_features,
    pca,
    pc_transform,
    tsvd,
    tsvd_transform,
    regress_out,
)
from .hvf_selection import estimate_feature_statistics, highly_variable_features
from .batch_correction import run_harmony, run_scanorama
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
from .pseudotime import calc_pseudotime, infer_path
from .clustering import (
    jump_method,
    louvain,
    leiden,
    spectral_louvain,
    spectral_leiden,
    cluster,
    split_one_cluster,
    calc_dendrogram,
)
from .net_regressor import net_train_and_predict
from .visualization import (
    tsne,
    umap,
    fle,
    net_umap,
    net_fle,
)
from .diff_expr import (
    de_analysis,
    markers,
    write_results_to_excel,
    cluster_specific_markers,
    run_de_analysis,
)
from .gradient_boosting import find_markers, run_find_markers
from .subcluster_utils import clone_subset
from .signature_score import calc_signature_score, calculate_z_score
from .doublet_detection import infer_doublets, mark_doublets
from .nmf import nmf, integrative_nmf, find_nmf_programs
from .pseudobulk import pseudobulk, deseq2
from .gsea import gsea, write_gsea_results_to_excel
from .scvitools import (
    run_scvi,
    train_scarches_scanvi,
    predict_scarches_scanvi,
)
