from .pca import pca, pca_loadings
from .neighbors import neighbors
from .clustering import (
    cluster, cluster_metrics, categorical_confusion,
    leiden_resolution_scan,
    )

from .umap import umap, umap_graph
from .de import de
from .de_glm import de_glm
from .rank_genes_groups import rank_genes_groups
from .adjusted_rand_index import adjusted_rand_index
from .score_genes import score_genes, score_genes_dict, score_genes_cell_cycle

from .tcga_groups import tcga_define_groups
from .dispersion import sample_dispersion, signature_dispersion_by_group

from .metaprograms import (
    read_metaprograms_xlsx, score_metaprograms, 
    mp_dispersion_metrics, metaprogram_heterogeneity,
    summarize_by_group,
    metaprogram_scores_get, metaprogram_sample_metrics,
    metaprogram_dispersion_by_group, metaprogram_ne_enrichment,
    metaprogram_topk_contribution,
    )

from .correlations import (
    top_gene_gene_correlations, gene_gene_correlations,
    top_gene_obs_correlations, top_obs_obs_correlations, 
    obs_obs_corr_matrix, partial_corr,
    plot_corr_scatter, plot_corr_heatmap,
    )
from .associations import (
    association,
    gene_categorical_association,
    rank_genes_groups_fast,
    categorical_association,
    store_gene_categorical_association,
    store_rank_genes_groups_fast,
    posthoc_per_gene,
    gene_metadata_association_scan, signature_axis, quantile_groups,
    )

from .posthoc import pairwise_posthoc

from .cox import (
    cox_gene_association, cox_multivariate,
    cox_penalizer_cv, cox_stability_selection, 
    panel_size_cindex, recommended_cox_panel,
    cox_fit_penalized, 
    cox_univariate, cox_interaction, 
    surv_1d_bins, surv_2x2_bins,
    )

from .signature import (
    filter_genes_var, rank_genes_univariate_pr, gene_corr_redundancy,
    signature_score, validate_signature_external, validate_signature_auc_external,
    design_signatures, signature_permutation_importance,
    correlation_redundancy_filter, redundancy_filter_by_corr,
    meta_rank_genes_from_signatures,
    recommended_auc_panel,
    make_signature_frozen, quick_fit_weights, add_signature_from_genes,
    benchmark_signatures_pr_auc, fit_intercept_only,
    evaluate_signatures_store, pick_best_signature,
    score_signature_on_PPV, add_signature_from_genes,
    save_signature_bank, load_signature_bank, 
    build_signature_bank_from_genes,
    )

from .gsea_prerank import gsea_preranked, list_enrichr_libraries

__all__ = ["pca", "neighbors", "cluster", "umap",
           "umap_graph", "de", "de_glm", "pca_loadings",
           "rank_genes_groups", "adjusted_rand_index",
           "cluster_metrics", "leiden_resolution_scan",
           "categorical_confusion",
           "score_genes", "score_genes_dict", "score_genes_cell_cycle",
           "top_gene_gene_correlations", "top_gene_obs_correlations",
           "top_obs_obs_correlations", "gene_gene_correlations",
           "obs_obs_corr_matrix", "partial_corr",
           "plot_corr_scatter", "plot_corr_heatmap",
           "association",
           "gene_categorical_association", "rank_genes_groups_fast",
           "categorical_association", "store_gene_categorical_association",
           "store_rank_genes_groups_fast",
           "posthoc_per_gene",
           "pairwise_posthoc",
           "cox_gene_association", "cox_multivariate",
           "cox_penalizer_cv", "cox_stability_selection", 
           "panel_size_cindex", "recommended_cox_panel",
           "cox_fit_penalized", 
           "cox_univariate", "cox_interaction", 
           "surv_1d_bins", "surv_2x2_bins",
           "filter_genes_var", "rank_genes_univariate_pr", "gene_corr_redundancy",
           "signature_score", "validate_signature_external", 
           "validate_signature_auc_external", "design_signatures",
           "signature_permutation_importance", "correlation_redundancy_filter",
           "redundancy_filter_by_corr", "meta_rank_genes_from_signatures",
           "recommended_auc_panel", "make_signature_frozen",
           "quick_fit_weights", "fit_intercept_only",
           "benchmark_signatures_pr_auc", "add_signature_from_genes",
           "evaluate_signatures_store", "pick_best_signature",
           "score_signature_on_PPV", "add_signature_from_genes",
           "save_signature_bank", "load_signature_bank",
           "build_signature_bank_from_genes",
           "gsea_preranked", "list_enrichr_libraries",
           "tcga_define_groups",
           "sample_dispersion", "signature_dispersion_by_group",
           "read_metaprograms_xlsx", "score_metaprograms", 
           "mp_dispersion_metrics", "metaprogram_heterogeneity",
           "summarize_by_group",
           "signature_axis", "quantile_groups",
           "gene_metadata_association_scan",
           "metaprogram_scores_get", "metaprogram_sample_metrics",
           "metaprogram_dispersion_by_group", "metaprogram_ne_enrichment",
           "metaprogram_topk_contribution",
]