# Generated by roxygen2: do not edit by hand

S3method(get_expressed_genes,Seurat)
S3method(get_expressed_genes,default)
export(add_hyperparameters_parameter_settings)
export(add_ligand_popularity_measures_to_perfs)
export(add_new_datasource)
export(alias_to_symbol_seurat)
export(apply_hub_corrections)
export(assess_influence_source)
export(assess_rf_class_probabilities)
export(assign_ligands_to_celltype)
export(bootstrap_ligand_activity_analysis)
export(calculate_de)
export(calculate_fraction_top_predicted)
export(calculate_fraction_top_predicted_fisher)
export(calculate_niche_de)
export(calculate_niche_de_targets)
export(calculate_p_value_bootstrap)
export(calculate_spatial_DE)
export(classification_evaluation_continuous_pred_wrapper)
export(combine_sender_receiver_de)
export(construct_ligand_target_matrix)
export(construct_ligand_tf_matrix)
export(construct_model)
export(construct_random_model)
export(construct_tf_target_matrix)
export(construct_weighted_networks)
export(convert_alias_to_symbols)
export(convert_cluster_to_settings)
export(convert_expression_settings_evaluation)
export(convert_expression_settings_evaluation_regression)
export(convert_gene_list_settings_evaluation)
export(convert_human_to_mouse_symbols)
export(convert_mouse_to_human_symbols)
export(convert_settings_ligand_prediction)
export(convert_settings_tf_prediction)
export(convert_settings_topn_ligand_prediction)
export(convert_single_cell_expression_to_settings)
export(correct_topology_ppr)
export(diagrammer_format_signaling_graph)
export(estimate_source_weights_characterization)
export(evaluate_importances_ligand_prediction)
export(evaluate_ligand_prediction_per_bin)
export(evaluate_model)
export(evaluate_model_application)
export(evaluate_model_application_multi_ligand)
export(evaluate_model_cv)
export(evaluate_multi_ligand_target_prediction)
export(evaluate_multi_ligand_target_prediction_regression)
export(evaluate_random_model)
export(evaluate_single_importances_ligand_prediction)
export(evaluate_target_prediction)
export(evaluate_target_prediction_interprete)
export(evaluate_target_prediction_per_bin)
export(evaluate_target_prediction_regression)
export(extract_ligands_from_settings)
export(extract_top_fraction_ligands)
export(extract_top_fraction_targets)
export(extract_top_n_ligands)
export(extract_top_n_targets)
export(generate_info_tables)
export(generate_prioritization_tables)
export(get_active_ligand_receptor_network)
export(get_active_ligand_target_df)
export(get_active_ligand_target_matrix)
export(get_active_regulatory_network)
export(get_active_signaling_network)
export(get_expressed_genes)
export(get_exprs_avg)
export(get_lfc_celltype)
export(get_ligand_activities_targets)
export(get_ligand_signaling_path)
export(get_ligand_signaling_path_with_receptor)
export(get_ligand_slope_ligand_prediction_popularity)
export(get_ligand_target_links_oi)
export(get_multi_ligand_importances)
export(get_multi_ligand_importances_regression)
export(get_multi_ligand_rf_importances)
export(get_multi_ligand_rf_importances_regression)
export(get_ncitations_genes)
export(get_non_spatial_de)
export(get_optimized_parameters_nsga2r)
export(get_prioritization_tables)
export(get_single_ligand_importances)
export(get_single_ligand_importances_regression)
export(get_slope_ligand_popularity)
export(get_slope_target_gene_popularity)
export(get_slope_target_gene_popularity_ligand_prediction)
export(get_target_genes_ligand_oi)
export(get_top_predicted_genes)
export(get_weighted_ligand_receptor_links)
export(get_weighted_ligand_target_links)
export(infer_supporting_datasources)
export(ligand_activity_performance_top_i_removed)
export(make_circos_lr)
export(make_circos_plot)
export(make_discrete_ligand_target_matrix)
export(make_heatmap_bidir_lt_ggplot)
export(make_heatmap_ggplot)
export(make_ligand_activity_target_exprs_plot)
export(make_ligand_receptor_lfc_plot)
export(make_ligand_receptor_lfc_spatial_plot)
export(make_line_plot)
export(make_mushroom_plot)
export(make_threecolor_heatmap_ggplot)
export(mlrmbo_optimization)
export(model_based_ligand_activity_prediction)
export(model_evaluation_hyperparameter_optimization_mlrmbo)
export(model_evaluation_optimization_application)
export(model_evaluation_optimization_mlrmbo)
export(model_evaluation_optimization_nsga2r)
export(mutate_cond)
export(nichenet_seuratobj_aggregate)
export(nichenet_seuratobj_aggregate_cluster_de)
export(nichenet_seuratobj_cluster_de)
export(normalize_single_cell_ligand_activities)
export(predict_ligand_activities)
export(predict_single_cell_ligand_activities)
export(prepare_circos_visualization)
export(prepare_ligand_receptor_visualization)
export(prepare_ligand_target_visualization)
export(prepare_settings_leave_one_in_characterization)
export(prepare_settings_leave_one_out_characterization)
export(prepare_settings_one_vs_one_characterization)
export(process_characterization_ligand_prediction)
export(process_characterization_ligand_prediction_single_measures)
export(process_characterization_popularity_slopes_ligand_prediction)
export(process_characterization_popularity_slopes_target_prediction)
export(process_characterization_target_prediction)
export(process_characterization_target_prediction_average)
export(process_mlrmbo_nichenet_optimization)
export(process_niche_de)
export(process_receiver_target_de)
export(process_spatial_de)
export(process_table_to_ic)
export(randomize_complete_network_source_specific)
export(randomize_datasource_network)
export(randomize_network)
export(run_nsga2R_cluster)
export(scale_quantile)
export(scale_quantile_adapted)
export(scaling_modified_zscore)
export(scaling_zscore)
export(single_ligand_activity_score_classification)
export(single_ligand_activity_score_regression)
export(visualize_parameter_values)
export(visualize_parameter_values_across_folds)
export(wrapper_average_performances)
export(wrapper_evaluate_single_importances_ligand_prediction)
import(Seurat)
import(caret)
import(cowplot)
import(dplyr)
import(e1071)
import(ggforce)
import(ggnewscale)
import(ggplot2)
import(readr)
import(shadowtext)
import(tibble)
import(tidyr)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,draw)
importFrom(DiagrammeR,create_edge_df)
importFrom(DiagrammeR,create_graph)
importFrom(DiagrammeR,create_node_df)
importFrom(Hmisc,cut2)
importFrom(Matrix,sparseMatrix)
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(caTools,trapz)
importFrom(circlize,CELL_META)
importFrom(circlize,chordDiagram)
importFrom(circlize,circos.clear)
importFrom(circlize,circos.par)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(data.table,data.table)
importFrom(fdrtool,fdrtool)
importFrom(grDevices,recordPlot)
importFrom(igraph,V)
importFrom(igraph,degree)
importFrom(igraph,get.data.frame)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,page_rank)
importFrom(igraph,sample_degseq)
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(purrr,reduce)
importFrom(purrr,safely)
importFrom(randomForest,importance)
importFrom(randomForest,randomForest)
importFrom(tibble,tibble)