Files in saeyslab/nichenetr
NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R-raw/developing_package_light.R R/application_network_extraction.R R/application_prediction.R R/application_visualization.R R/calculate_popularity_bias.R R/characterization_data_sources.R R/construct_ligand_to_target.R R/construct_random_networks.R R/data.R R/evaluate_model_ligand_prediction.R R/evaluate_model_target_prediction.R R/nichenetr.R R/parameter_optimization.R R/supporting_functions.R R/use_ligand_to_target.R R/utils.R README.Rmd README.md
data/annotation_data_sources.rda
data/expression_settings_validation.rda
data/geneinfo_human.rda
data/gr_network.rda
data/hyperparameter_list.rda
data/lr_network.rda
data/ncitations.rda
data/optimized_source_weights_df.rda
data/sig_network.rda
data/source_weights_df.rda
inst/CITATION
man/add_hyperparameters_parameter_settings.Rd man/add_ligand_popularity_measures_to_perfs.Rd man/add_new_datasource.Rd man/annotation_data_sources.Rd man/apply_hub_corrections.Rd man/assess_influence_source.Rd man/assess_rf_class_probabilities.Rd man/calculate_fraction_top_predicted.Rd man/calculate_fraction_top_predicted_fisher.Rd man/classification_evaluation_continuous_pred_wrapper.Rd man/construct_ligand_target_matrix.Rd man/construct_ligand_tf_matrix.Rd man/construct_model.Rd man/construct_random_model.Rd man/construct_tf_target_matrix.Rd man/construct_weighted_networks.Rd man/convert_cluster_to_settings.Rd man/convert_expression_settings_evaluation.Rd man/convert_expression_settings_evaluation_regression.Rd man/convert_gene_list_settings_evaluation.Rd man/convert_human_to_mouse_symbols.Rd man/convert_mouse_to_human_symbols.Rd man/convert_settings_ligand_prediction.Rd man/convert_settings_tf_prediction.Rd man/convert_settings_topn_ligand_prediction.Rd man/convert_single_cell_expression_to_settings.Rd man/correct_topology_ppr.Rd man/diagrammer_format_signaling_graph.Rd man/estimate_source_weights_characterization.Rd man/evaluate_importances_ligand_prediction.Rd man/evaluate_ligand_prediction_per_bin.Rd man/evaluate_model.Rd man/evaluate_model_application.Rd man/evaluate_model_application_multi_ligand.Rd man/evaluate_model_cv.Rd man/evaluate_multi_ligand_target_prediction.Rd man/evaluate_multi_ligand_target_prediction_regression.Rd man/evaluate_random_model.Rd man/evaluate_single_importances_ligand_prediction.Rd man/evaluate_target_prediction.Rd man/evaluate_target_prediction_interprete.Rd man/evaluate_target_prediction_per_bin.Rd man/evaluate_target_prediction_regression.Rd man/expression_settings_validation.Rd man/extract_ligands_from_settings.Rd man/extract_top_fraction_ligands.Rd man/extract_top_fraction_targets.Rd man/extract_top_n_ligands.Rd man/extract_top_n_targets.Rd man/geneinfo_human.Rd man/get_active_ligand_receptor_network.Rd man/get_active_ligand_target_df.Rd man/get_active_ligand_target_matrix.Rd man/get_active_regulatory_network.Rd man/get_active_signaling_network.Rd man/get_expressed_genes.Rd man/get_lfc_celltype.Rd man/get_ligand_signaling_path.Rd man/get_ligand_slope_ligand_prediction_popularity.Rd man/get_multi_ligand_importances.Rd man/get_multi_ligand_importances_regression.Rd man/get_multi_ligand_rf_importances.Rd man/get_multi_ligand_rf_importances_regression.Rd man/get_ncitations_genes.Rd man/get_single_ligand_importances.Rd man/get_single_ligand_importances_regression.Rd man/get_slope_ligand_popularity.Rd man/get_slope_target_gene_popularity.Rd man/get_slope_target_gene_popularity_ligand_prediction.Rd man/get_target_genes_ligand_oi.Rd man/get_top_predicted_genes.Rd man/get_weighted_ligand_target_links.Rd man/gr_network.Rd man/hyperparameter_list.Rd man/infer_supporting_datasources.Rd man/ligand_activity_performance_top_i_removed.Rd man/lr_network.Rd man/make_discrete_ligand_target_matrix.Rd man/make_heatmap_bidir_lt_ggplot.Rd man/make_heatmap_ggplot.Rd man/make_threecolor_heatmap_ggplot.Rd man/mlrmbo_optimization.Rd man/model_based_ligand_activity_prediction.Rd man/model_evaluation_hyperparameter_optimization.Rd man/model_evaluation_optimization.Rd man/model_evaluation_optimization_application.Rd man/ncitations.Rd man/nichenet_seuratobj_aggregate.Rd man/nichenet_seuratobj_aggregate_cluster_de.Rd man/nichenet_seuratobj_cluster_de.Rd man/nichenetr.Rd man/normalize_single_cell_ligand_activities.Rd man/optimized_source_weights_df.Rd man/predict_ligand_activities.Rd man/predict_single_cell_ligand_activities.Rd man/prepare_ligand_target_visualization.Rd man/prepare_settings_leave_one_in_characterization.Rd man/prepare_settings_leave_one_out_characterization.Rd man/prepare_settings_one_vs_one_characterization.Rd man/process_characterization_ligand_prediction.Rd man/process_characterization_ligand_prediction_single_measures.Rd man/process_characterization_popularity_slopes_ligand_prediction.Rd man/process_characterization_popularity_slopes_target_prediction.Rd man/process_characterization_target_prediction.Rd man/process_characterization_target_prediction_average.Rd man/process_mlrmbo_nichenet_optimization.Rd man/randomize_complete_network_source_specific.Rd man/randomize_datasource_network.Rd man/randomize_network.Rd man/scale_quantile.Rd man/scaling_modified_zscore.Rd man/scaling_zscore.Rd man/sig_network.Rd man/single_ligand_activity_score_classification.Rd man/single_ligand_activity_score_regression.Rd man/source_weights_df.Rd man/wrapper_average_performances.Rd man/wrapper_evaluate_single_importances_ligand_prediction.Rd
nichenetr.Rproj
tests/test_application.R tests/test_characterization.R tests/test_general_functions.R tests/test_ligand_prediction.R tests/test_model_construction.R tests/test_optimization.R tests/test_target_prediction.R tests/testthat/Rplots.pdf tests/testthat/test-application_networks.R tests/testthat/test-application_prediction.R tests/testthat/test-application_visualization.R tests/testthat/test-calculate_popularity_bias.R tests/testthat/test-characterization.R tests/testthat/test-construct_ligand_to_target.R tests/testthat/test-evaluate_model_ligand_prediction.R tests/testthat/test-evaluate_model_target_prediction.R tests/testthat/test-optimization.R tests/testthat/test-random_networks.R tests/testthat/test-use_ligand_to_target.R
vignettes/.gitignore
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saeyslab/nichenetr documentation built on July 9, 2020, 2:46 p.m.