Files in saeyslab/nichenetr
Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet
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.github/.gitignore
.github/workflows/check-bioc.yml
.github/workflows/check-standard.yaml
.gitignore
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/differential_nichenet.R
R/differential_nichenet_plotting.R
R/evaluate_model_ligand_prediction.R
R/evaluate_model_target_prediction.R
R/nichenetr-package.R
R/parameter_optimization.R
R/prioritization.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_2022.rda
data/geneinfo_alias_human.rda
data/geneinfo_alias_mouse.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/alias_to_symbol_seurat.Rd
man/annotation_data_sources.Rd
man/apply_hub_corrections.Rd
man/assess_influence_source.Rd
man/assess_rf_class_probabilities.Rd
man/assign_ligands_to_celltype.Rd
man/bootstrap_ligand_activity_analysis.Rd
man/calculate_de.Rd
man/calculate_fraction_top_predicted.Rd
man/calculate_fraction_top_predicted_fisher.Rd
man/calculate_niche_de.Rd
man/calculate_niche_de_targets.Rd
man/calculate_p_value_bootstrap.Rd
man/calculate_spatial_DE.Rd
man/classification_evaluation_continuous_pred_wrapper.Rd
man/combine_sender_receiver_de.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_alias_to_symbols.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_2022.Rd
man/geneinfo_alias_human.Rd
man/geneinfo_alias_mouse.Rd
man/geneinfo_human.Rd
man/generate_info_tables.Rd
man/generate_prioritization_tables.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_exprs_avg.Rd
man/get_lfc_celltype.Rd
man/get_ligand_activities_targets.Rd
man/get_ligand_signaling_path.Rd
man/get_ligand_signaling_path_with_receptor.Rd
man/get_ligand_slope_ligand_prediction_popularity.Rd
man/get_ligand_target_links_oi.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_non_spatial_de.Rd
man/get_optimized_parameters_nsga2r.Rd
man/get_prioritization_tables.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_receptor_links.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_circos_lr.Rd
man/make_circos_plot.Rd
man/make_discrete_ligand_target_matrix.Rd
man/make_heatmap_bidir_lt_ggplot.Rd
man/make_heatmap_ggplot.Rd
man/make_ligand_activity_target_exprs_plot.Rd
man/make_ligand_receptor_lfc_plot.Rd
man/make_ligand_receptor_lfc_spatial_plot.Rd
man/make_line_plot.Rd
man/make_mushroom_plot.Rd
man/make_threecolor_heatmap_ggplot.Rd
man/mlrmbo_optimization.Rd
man/model_based_ligand_activity_prediction.Rd
man/model_evaluation_hyperparameter_optimization_mlrmbo.Rd
man/model_evaluation_optimization_application.Rd
man/model_evaluation_optimization_mlrmbo.Rd
man/model_evaluation_optimization_nsga2r.Rd
man/mutate_cond.Rd
man/ncitations.Rd
man/nichenet_seuratobj_aggregate.Rd
man/nichenet_seuratobj_aggregate_cluster_de.Rd
man/nichenet_seuratobj_cluster_de.Rd
man/nichenetr-package.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_circos_visualization.Rd
man/prepare_ligand_receptor_visualization.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/process_niche_de.Rd
man/process_receiver_target_de.Rd
man/process_spatial_de.Rd
man/process_table_to_ic.Rd
man/randomize_complete_network_source_specific.Rd
man/randomize_datasource_network.Rd
man/randomize_network.Rd
man/run_nsga2R_cluster.Rd
man/scale_quantile.Rd
man/scale_quantile_adapted.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/visualize_parameter_values.Rd
man/visualize_parameter_values_across_folds.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_prioritization.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-differential_nichenet.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-prioritization.R
tests/testthat/test-random_networks.R
tests/testthat/test-symbol_conversion.R
tests/testthat/test-use_ligand_to_target.R
vignettes/.gitignore
vignettes/circos.Rmd
vignettes/circos.md
vignettes/circos_files/figure-gfm/double-circos-method-1-1.png
vignettes/circos_files/figure-gfm/double-circos-method-2-1.png
vignettes/circos_files/figure-gfm/ligand-receptor-circos-1.png
vignettes/circos_files/figure-gfm/ligand-receptor-circos-transparent-1.png
vignettes/circos_files/figure-gfm/ligand-target-circos-1.png
vignettes/circos_files/figure-gfm/ligand-target-circos-transparent-1.png
vignettes/circos_files/figure-gfm/ligand-target-circos-unused-1.png
vignettes/circos_files/figure-gfm/ligand-target-circos-with-legend-1.png
vignettes/data_sources.xlsx
vignettes/differential_nichenet.Rmd
vignettes/differential_nichenet.md
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-65-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-86-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-87-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-88-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-89-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-90-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-91-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-91-2.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-92-1.png
vignettes/differential_nichenet_files/figure-gfm/unnamed-chunk-93-1.png
vignettes/differential_nichenet_pEMT.Rmd
vignettes/differential_nichenet_pEMT.md
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-2-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-2-2.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-28-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-29-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-30-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-31-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-32-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-32-2.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-33-1.png
vignettes/differential_nichenet_pEMT_files/figure-gfm/unnamed-chunk-4-1.png
vignettes/evaluation_datasets.xlsx
vignettes/faq.Rmd
vignettes/faq.md
vignettes/images/circos_plot_adapted.jpg
vignettes/images/circos_plot_adapted.png
vignettes/images/comparison_other_approaches_2.jpg
vignettes/images/figure1.svg
vignettes/images/figure2.svg
vignettes/images/ligand_activity_prediction_workflow_new.png
vignettes/images/nichenet_prior_model.png
vignettes/images/workflow_model_construction.png
vignettes/images/workflow_nichenet.jpg
vignettes/images/workflow_nichenet.png
vignettes/library.bib
vignettes/ligand_activity_geneset.Rmd
vignettes/ligand_activity_geneset.md
vignettes/ligand_activity_geneset_files/figure-gfm/ligand-activity-heatmap-1.png
vignettes/ligand_activity_geneset_files/figure-gfm/ligand-expression-heatmap-1.png
vignettes/ligand_activity_geneset_files/figure-gfm/ligand-receptor-heatmap-1.png
vignettes/ligand_activity_geneset_files/figure-gfm/ligand-target-heatmap-1.png
vignettes/ligand_activity_geneset_files/figure-gfm/summary-vis-1.png
vignettes/ligand_activity_geneset_files/figure-gfm/target-expression-heatmap-1.png
vignettes/ligand_activity_single_cell.Rmd
vignettes/ligand_activity_single_cell.md
vignettes/ligand_activity_single_cell_files/figure-gfm/scatterplot-1.png
vignettes/ligand_target_signaling_path.Rmd
vignettes/ligand_target_signaling_path.md
vignettes/ligand_target_signaling_path_files/figure-gfm/signaling-graph-1.png
vignettes/model_construction.Rmd
vignettes/model_construction.md
vignettes/model_construction_with_liana.Rmd
vignettes/model_construction_with_liana.md
vignettes/model_construction_with_liana_files/figure-gfm/line-plot-1.png
vignettes/model_evaluation.Rmd
vignettes/model_evaluation.md
vignettes/model_evaluation_files/figure-gfm/ligand-activity-comparison-1.png
vignettes/model_evaluation_files/figure-gfm/ligand-activity-v2-results-1.png
vignettes/model_evaluation_files/figure-gfm/target-prediction-comparison-1.png
vignettes/model_evaluation_files/figure-gfm/target-prediction-v2-results-1.png
vignettes/parameter_optimization.Rmd
vignettes/parameter_optimization.md
vignettes/parameter_optimization_files/figure-gfm/weights-between-folds-1.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-folds-2.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-folds-3.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-folds-4.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-1.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-10.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-2.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-3.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-4.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-5.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-6.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-7.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-8.png
vignettes/parameter_optimization_files/figure-gfm/weights-between-populations-9.png
vignettes/seurat_steps.Rmd
vignettes/seurat_steps.md
vignettes/seurat_steps_files/figure-gfm/agnostic-ligand-activity-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/dotplot-1.png
vignettes/seurat_steps_files/figure-gfm/focused-ligand-activity-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/focused-ligand-receptor-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/focused-ligand-target-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/histogram-1.png
vignettes/seurat_steps_files/figure-gfm/lfc-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/ligand-receptor-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/ligand-target-heatmap-1.png
vignettes/seurat_steps_files/figure-gfm/lineplot-1.png
vignettes/seurat_steps_files/figure-gfm/summary-vis-1.png
vignettes/seurat_steps_files/figure-gfm/umap-1-1.png
vignettes/seurat_steps_files/figure-gfm/umap-2-1.png
vignettes/seurat_steps_prioritization.Rmd
vignettes/seurat_steps_prioritization.md
vignettes/seurat_steps_prioritization_files/figure-gfm/lr-circos-1.png
vignettes/seurat_steps_prioritization_files/figure-gfm/lr-circos-unused-1.png
vignettes/seurat_steps_prioritization_files/figure-gfm/lr-circos-unused-2.png
vignettes/seurat_steps_prioritization_files/figure-gfm/mushroom-plot-1-1.png
vignettes/seurat_steps_prioritization_files/figure-gfm/mushroom-plot-2-1.png
vignettes/seurat_wrapper.Rmd
vignettes/seurat_wrapper.md
vignettes/seurat_wrapper_circos.Rmd
vignettes/seurat_wrapper_circos.md
vignettes/seurat_wrapper_circos_files/figure-gfm/dotplot-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/lfc-heatmap-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-receptor-circos-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-target-circos-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-target-circos-transparent-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-target-circos-unused-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-target-circos-with-legend-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/ligand-target-heatmap-1.png
vignettes/seurat_wrapper_circos_files/figure-gfm/violin-plot-1.png
vignettes/seurat_wrapper_files/figure-gfm/dotplot-cluster-de-1.png
vignettes/seurat_wrapper_files/figure-gfm/dotplot-condition-1.png
vignettes/seurat_wrapper_files/figure-gfm/dotplot-receptors-1.png
vignettes/seurat_wrapper_files/figure-gfm/dotplot-sender-1.png
vignettes/seurat_wrapper_files/figure-gfm/lfc-heatmap-1.png
vignettes/seurat_wrapper_files/figure-gfm/ligand-receptor-heatmap-1.png
vignettes/seurat_wrapper_files/figure-gfm/ligand-target-heatmap-1.png
vignettes/seurat_wrapper_files/figure-gfm/ligand-target-heatmap-adapted-1.png
vignettes/seurat_wrapper_files/figure-gfm/summary-vis-1.png
vignettes/seurat_wrapper_files/figure-gfm/summary-vis-agnostic-1.png
vignettes/seurat_wrapper_files/figure-gfm/summary-vis-cluster-de-1.png
vignettes/seurat_wrapper_files/figure-gfm/umap-1-1.png
vignettes/seurat_wrapper_files/figure-gfm/umap-2-1.png
vignettes/seurat_wrapper_files/figure-gfm/violin-plot-1.png
vignettes/symbol_conversion.Rmd
vignettes/symbol_conversion.md
vignettes/target_prediction_evaluation_geneset.Rmd
vignettes/target_prediction_evaluation_geneset.md
