API for saeyslab/nichenetr
NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Global functions
.calcAUC Source code
PPR_wrapper Source code
SPL_wrapper Source code
add_hyperparameters_parameter_settings Man page Source code
add_ligand_popularity_measures_to_perfs Man page Source code
add_new_datasource Man page Source code
annotation_data_sources Man page
apply_hub_corrections Man page Source code
assess_influence_source Man page Source code
assess_rf_class_probabilities Man page Source code
cal_diffexp Source code
calculate_auc_iregulon Source code
calculate_fraction_top_predicted Man page Source code
calculate_fraction_top_predicted_fisher Man page Source code
caret_classification_evaluation_continuous Source code
classification_evaluation_categorical_pred Source code
classification_evaluation_continuous_pred Source code
classification_evaluation_continuous_pred_wrapper Man page Source code
construct_ligand_target_matrix Man page Source code
construct_ligand_tf_matrix Man page Source code
construct_model Man page Source code
construct_random_model Man page
construct_tf_target_matrix Man page Source code
construct_weighted_networks Man page Source code
convert_cluster_to_settings Man page Source code
convert_expression_settings_evaluation Man page Source code
convert_expression_settings_evaluation_regression Man page Source code
convert_gene_list_settings_evaluation Man page Source code
convert_human_to_mouse_symbols Man page Source code
convert_mouse_to_human_symbols Man page Source code
convert_settings_ligand_prediction Man page Source code
convert_settings_tf_prediction Man page Source code
convert_settings_topn_ligand_prediction Man page Source code
convert_single_cell_expression_to_settings Man page Source code
correct_topology_ppr Man page Source code
diagrammer_format_signaling_graph Man page Source code
direct_wrapper Source code
estimate_source_weights_characterization Man page
evaluate_importances_ligand_prediction Man page Source code
evaluate_ligand_prediction_per_bin Man page Source code
evaluate_model Man page Source code
evaluate_model_application Man page Source code
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
evaluate_random_model Man page
evaluate_single_importances_ligand_prediction Man page Source code
evaluate_target_prediction Man page Source code
evaluate_target_prediction_bins_direct Source code
evaluate_target_prediction_interprete Man page Source code
evaluate_target_prediction_per_bin Man page Source code
evaluate_target_prediction_regression Man page Source code
evaluate_target_prediction_strict Source code
expression_settings_validation Man page
extract_ligands_from_settings Man page Source code
extract_top_fraction_ligands Man page Source code
extract_top_fraction_targets Man page Source code
extract_top_n_ligands Man page Source code
extract_top_n_targets Man page Source code
geneinfo_human 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_design Source code
get_expressed_genes Man page Source code
get_lfc_celltype Man page Source code
get_ligand_signaling_path Man page Source code
get_ligand_slope_ligand_prediction_popularity Man page Source code
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_pagerank_target 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_split_auroc Source code
get_target_genes_ligand_oi Man page Source code
get_top_predicted_genes 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
lr_network Man page
make_diffexp_timeseries Source code
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_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 Man page Source code
model_evaluation_optimization Man page Source code
model_evaluation_optimization_application Man page
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
normalize_single_cell_ligand_activities Man page 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_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
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
randomize_complete_network_source_specific Man page Source code
randomize_datasource_network Man page Source code
randomize_network Man page Source code
rank_desc Source code
scale_quantile 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
single_ligand_ppr_wrapper Source code
source_weights_df Man page
wrapper_average_performances Man page Source code
wrapper_evaluate_single_importances_ligand_prediction Man page Source code
saeyslab/nichenetr documentation built on July 9, 2020, 2:46 p.m.