| activity_plot |
Source code
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| add_hyperparameters_parameter_settings |
Man page
Source code
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| add_ligand_popularity_measures_to_perfs |
Man page
Source code
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| add_new_datasource |
Man page
Source code
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| alias_to_symbol_seurat |
Man page
Source code
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| annotation_data_sources |
Man page
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| apply_hub_corrections |
Man page
Source code
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| assess_influence_source |
Man page
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| assess_rf_class_probabilities |
Man page
Source code
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| assign_ligands_to_celltype |
Man page
Source code
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| bootstrap_ligand_activity_analysis |
Man page
Source code
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| calculate_de |
Man page
Source code
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| calculate_fraction_top_predicted |
Man page
Source code
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| calculate_fraction_top_predicted_fisher |
Man page
Source code
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| calculate_niche_de |
Man page
Source code
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| calculate_niche_de_targets |
Man page
Source code
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| calculate_p_value_bootstrap |
Man page
Source code
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| calculate_spatial_DE |
Man page
Source code
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| check_names |
Source code
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| classification_evaluation_continuous_pred_wrapper |
Man page
Source code
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| combine_sender_receiver_de |
Man page
Source code
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| construct_ligand_target_matrix |
Man page
Source code
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| construct_ligand_tf_matrix |
Man page
Source code
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| construct_model |
Man page
Source code
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| construct_random_model |
Man page
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| construct_tf_target_matrix |
Man page
Source code
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| construct_weighted_networks |
Man page
Source code
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| convert_alias_to_symbols |
Man page
Source code
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| convert_cluster_to_settings |
Man page
Source code
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| convert_expression_settings_evaluation |
Man page
Source code
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| convert_expression_settings_evaluation_regression |
Man page
Source code
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| convert_gene_list_settings_evaluation |
Man page
Source code
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| convert_human_to_mouse_symbols |
Man page
Source code
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| convert_mouse_to_human_symbols |
Man page
Source code
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| convert_settings_ligand_prediction |
Man page
Source code
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| convert_settings_tf_prediction |
Man page
Source code
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| convert_settings_topn_ligand_prediction |
Man page
Source code
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| convert_single_cell_expression_to_settings |
Man page
Source code
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| correct_topology_ppr |
Man page
Source code
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| diagrammer_format_signaling_graph |
Man page
Source code
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| estimate_source_weights_characterization |
Man page
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| evaluate_importances_ligand_prediction |
Man page
Source code
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| evaluate_ligand_prediction_per_bin |
Man page
Source code
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| evaluate_model |
Man page
Source code
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| evaluate_model_application |
Man page
Source code
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| evaluate_model_application_multi_ligand |
Man page
|
| evaluate_model_cv |
Man page
|
| evaluate_multi_ligand_target_prediction |
Man page
Source code
|
| evaluate_multi_ligand_target_prediction_regression |
Man page
Source code
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| evaluate_random_model |
Man page
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| evaluate_single_importances_ligand_prediction |
Man page
Source code
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| evaluate_target_prediction |
Man page
Source code
|
| evaluate_target_prediction_interprete |
Man page
Source code
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| evaluate_target_prediction_per_bin |
Man page
Source code
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| evaluate_target_prediction_regression |
Man page
Source code
|
| expression_settings_validation |
Man page
|
| extract_ligands_from_settings |
Man page
Source code
|
| extract_top_fraction_ligands |
Man page
Source code
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| extract_top_fraction_targets |
Man page
Source code
|
| extract_top_n_ligands |
Man page
Source code
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| extract_top_n_targets |
Man page
Source code
|
| geneinfo_2022 |
Man page
|
| geneinfo_alias_human |
Man page
|
| geneinfo_alias_mouse |
Man page
|
| geneinfo_human |
Man page
|
| generate_info_tables |
Man page
|
| generate_prioritization_tables |
Man page
|
| get_active_ligand_receptor_network |
Man page
Source code
|
| get_active_ligand_target_df |
Man page
Source code
|
| get_active_ligand_target_matrix |
Man page
Source code
|
| get_active_regulatory_network |
Man page
Source code
|
| get_active_signaling_network |
Man page
Source code
|
| get_expressed_genes |
Man page
Source code
|
| get_expressed_genes.Seurat |
Man page
Source code
|
| get_expressed_genes.default |
Man page
Source code
|
| get_exprs_avg |
Man page
Source code
|
| get_lfc_celltype |
Man page
Source code
|
| get_ligand_activities_targets |
Man page
Source code
|
| get_ligand_signaling_path |
Man page
Source code
|
| get_ligand_signaling_path_with_receptor |
Man page
|
| get_ligand_slope_ligand_prediction_popularity |
Man page
Source code
|
| get_ligand_target_links_oi |
Man page
|
| get_multi_ligand_importances |
Man page
Source code
|
| get_multi_ligand_importances_regression |
Man page
Source code
|
| get_multi_ligand_rf_importances |
Man page
Source code
|
| get_multi_ligand_rf_importances_regression |
Man page
Source code
|
| get_ncitations_genes |
Man page
Source code
|
| get_non_spatial_de |
Man page
Source code
|
| get_optimized_parameters_nsga2r |
Man page
|
| get_prioritization_tables |
Man page
Source code
|
| get_single_ligand_importances |
Man page
Source code
|
| get_single_ligand_importances_regression |
Man page
Source code
|
| get_slope_ligand_popularity |
Man page
Source code
|
| get_slope_target_gene_popularity |
Man page
Source code
|
| get_slope_target_gene_popularity_ligand_prediction |
Man page
Source code
|
| get_target_genes_ligand_oi |
Man page
Source code
|
| get_top_predicted_genes |
Man page
Source code
|
| get_weighted_ligand_receptor_links |
Man page
Source code
|
| get_weighted_ligand_target_links |
Man page
Source code
|
| gr_network |
Man page
|
| hyperparameter_list |
Man page
|
| infer_supporting_datasources |
Man page
Source code
|
| ligand_activity_performance_top_i_removed |
Man page
Source code
|
| ligand_lfc_plot |
Source code
|
| ligand_lfc_spatial_plot |
Source code
|
| lr_network |
Man page
|
| make_circos_lr |
Man page
Source code
|
| make_circos_plot |
Man page
|
| make_discrete_ligand_target_matrix |
Man page
Source code
|
| make_heatmap_bidir_lt_ggplot |
Man page
Source code
|
| make_heatmap_ggplot |
Man page
Source code
|
| make_ligand_activity_target_exprs_plot |
Man page
Source code
|
| make_ligand_receptor_lfc_plot |
Man page
Source code
|
| make_ligand_receptor_lfc_spatial_plot |
Man page
Source code
|
| make_line_plot |
Man page
|
| make_mushroom_plot |
Man page
Source code
|
| make_threecolor_heatmap_ggplot |
Man page
Source code
|
| mapper |
Source code
Source code
|
| mlrmbo_optimization |
Man page
Source code
|
| model_based_ligand_activity_prediction |
Man page
Source code
|
| model_evaluation_hyperparameter_optimization_mlrmbo |
Man page
Source code
|
| model_evaluation_optimization_application |
Man page
|
| model_evaluation_optimization_mlrmbo |
Man page
Source code
|
| model_evaluation_optimization_nsga2r |
Man page
|
| mutate_cond |
Man page
Source code
|
| ncitations |
Man page
|
| nichenet_seuratobj_aggregate |
Man page
Source code
|
| nichenet_seuratobj_aggregate_cluster_de |
Man page
Source code
|
| nichenet_seuratobj_cluster_de |
Man page
Source code
|
| nichenetr |
Man page
|
| nichenetr-package |
Man page
|
| normalize_single_cell_ligand_activities |
Man page
Source code
|
| normalized_activity_plot |
Source code
|
| optimized_source_weights_df |
Man page
|
| predict_ligand_activities |
Man page
Source code
|
| predict_single_cell_ligand_activities |
Man page
Source code
|
| prepare_circos_visualization |
Man page
|
| prepare_ligand_receptor_visualization |
Man page
Source code
|
| prepare_ligand_target_visualization |
Man page
Source code
|
| prepare_settings_leave_one_in_characterization |
Man page
Source code
|
| prepare_settings_leave_one_out_characterization |
Man page
Source code
|
| prepare_settings_one_vs_one_characterization |
Man page
Source code
|
| prioritization_score_plot |
Source code
|
| process_characterization_ligand_prediction |
Man page
Source code
|
| process_characterization_ligand_prediction_single_measures |
Man page
Source code
|
| process_characterization_popularity_slopes_ligand_prediction |
Man page
Source code
|
| process_characterization_popularity_slopes_target_prediction |
Man page
Source code
|
| process_characterization_target_prediction |
Man page
Source code
|
| process_characterization_target_prediction_average |
Man page
Source code
|
| process_mlrmbo_nichenet_optimization |
Man page
Source code
|
| process_niche_de |
Man page
Source code
|
| process_receiver_target_de |
Man page
Source code
|
| process_spatial_de |
Man page
Source code
|
| process_table_to_ic |
Man page
Source code
|
| randomize_complete_network_source_specific |
Man page
Source code
|
| randomize_datasource_network |
Man page
Source code
|
| randomize_network |
Man page
Source code
|
| receptor_lfc_plot |
Source code
|
| run_nsga2R_cluster |
Man page
|
| scale_quantile |
Man page
Source code
|
| scale_quantile_adapted |
Man page
Source code
|
| scaling_modified_zscore |
Man page
|
| scaling_zscore |
Man page
Source code
|
| sig_network |
Man page
|
| single_ligand_activity_score_classification |
Man page
Source code
|
| single_ligand_activity_score_regression |
Man page
Source code
Source code
|
| source_weights_df |
Man page
|
| visualize_parameter_values |
Man page
|
| visualize_parameter_values_across_folds |
Man page
|
| wrapper_average_performances |
Man page
Source code
|
| wrapper_evaluate_single_importances_ligand_prediction |
Man page
Source code
|
