Man pages for saeyslab/nichenetr
Linking Extracellular Protein Signals to Target Genes

add_hyperparameters_parameter_settingsAdd hyperparameters to existing parameter settings
add_ligand_popularity_measures_to_perfsMerge target gene prediction performances with popularity...
add_new_datasourceAdd a new data source to the model
annotation_data_sourcesAnnotation table of all data sources used in the NicheNet...
apply_hub_correctionsApply hub corrections to the weighted integrated...
assess_influence_sourceAssess the influence of an individual data source on...
assess_rf_class_probabilitiesAssess probability that a target gene belongs to the geneset...
calculate_fraction_top_predictedDetermine the fraction of genes belonging to the geneset or...
calculate_fraction_top_predicted_fisherPerform a Fisher's exact test to determine whether genes...
classification_evaluation_continuous_pred_wrapperAssess how well classification predictions accord to the...
construct_ligand_target_matrixConstruct a ligand-target probability matrix for ligands of...
construct_ligand_tf_matrixConstruct a ligand-tf signaling probability matrix for...
construct_modelConstruct a ligand-target model given input parameters.
construct_random_modelConstruct a randomised ligand-target model given input...
construct_tf_target_matrixConstruct a tf-target matrix.
construct_weighted_networksConstruct weighted layer-specific networks
convert_cluster_to_settingsConvert cluster assignment to settings format suitable for...
convert_expression_settings_evaluationConvert expression settings to correct settings format for...
convert_expression_settings_evaluation_regressionConvert expression settings to correct settings format for...
convert_gene_list_settings_evaluationConvert gene list to correct settings format for evaluation...
convert_human_to_mouse_symbolsConvert human gene symbols to their mouse one-to-one...
convert_mouse_to_human_symbolsConvert mouse gene symbols to their human one-to-one...
convert_settings_ligand_predictionConvert settings to correct settings format for ligand...
convert_settings_tf_predictionConvert settings to correct settings format for TF...
convert_settings_topn_ligand_predictionConverts expression settings to format in which the total...
convert_single_cell_expression_to_settingsPrepare single-cell expression data to perform ligand...
correct_topology_pprAdapt a ligand-target probability matrix construced via PPR...
diagrammer_format_signaling_graphPrepare extracted ligand-target signaling network for...
estimate_source_weights_characterizationEstimate data source weights of data sources of interest...
evaluate_importances_ligand_predictionEvaluation of ligand activity prediction based on ligand...
evaluate_ligand_prediction_per_binEvaluate ligand activity predictions for different...
evaluate_modelConstruct and evaluate a ligand-target model given input...
evaluate_model_applicationConstruct and evaluate a ligand-target model given input...
evaluate_model_application_multi_ligandConstruct and evaluate a ligand-target model given input...
evaluate_model_cvConstruct and evaluate a ligand-target model given input...
evaluate_multi_ligand_target_predictionEvaluation of target gene prediction for multiple ligands.
evaluate_multi_ligand_target_prediction_regressionEvaluation of target gene value prediction for multiple...
evaluate_random_modelConstruct and evaluate a randomised ligand-target model given...
evaluate_single_importances_ligand_predictionEvaluation of ligand activity prediction performance of...
evaluate_target_predictionEvaluation of target gene prediction.
evaluate_target_prediction_interpreteEvaluation of target gene prediction.
evaluate_target_prediction_per_binEvaluate target gene predictions for different bins/groups of...
evaluate_target_prediction_regressionEvaluation of target gene value prediction (regression).
expression_settings_validationExpression datasets for validation
extract_ligands_from_settingsExtract ligands of interest from settings
extract_top_fraction_ligandsGet the predicted top n percentage ligands of a target of...
extract_top_fraction_targetsGet the predicted top n percentage target genes of a ligand...
extract_top_n_ligandsGet the predicted top n ligands of a target gene of interest
extract_top_n_targetsGet the predicted top n target genes of a ligand of interest
geneinfo_humanGene annotation information
get_active_ligand_receptor_networkGet active ligand-receptor network for cellular interaction...
get_active_ligand_target_dfGet active ligand-target network in data frame format.
get_active_ligand_target_matrixGet active ligand-target matrix.
get_active_regulatory_networkGet active gene regulatory network in a receiver cell.
get_active_signaling_networkGet active signaling network in a receiver cell.
get_ligand_signaling_pathGet ligand-target signaling paths between ligand(s) and...
get_ligand_slope_ligand_prediction_popularityRegression analysis between popularity of left-out ligands...
get_multi_ligand_importancesGet ligand importances from a multi-ligand classfication...
get_multi_ligand_importances_regressionGet ligand importances from a multi-ligand regression model.
get_multi_ligand_rf_importancesGet ligand importances from a multi-ligand trained random...
get_multi_ligand_rf_importances_regressionGet ligand importances from a multi-ligand trained random...
get_ncitations_genesGet the number of times of gene is mentioned in the pubmed...
get_single_ligand_importancesGet ligand importances based on target gene prediction...
get_single_ligand_importances_regressionGet ligand importances based on target gene value prediction...
get_slope_ligand_popularityRegression analysis between ligand popularity and target gene...
get_slope_target_gene_popularityRegression analysis between target gene popularity and target...
get_slope_target_gene_popularity_ligand_predictionRegression analysis between target gene popularity and ligand...
get_target_genes_ligand_oiGet a set of predicted target genes of a ligand of interest
get_top_predicted_genesFind which genes were among the top-predicted targets genes...
get_weighted_ligand_target_linksInfer weighted active ligand-target links between a possible...
gr_networkGene regulatory network
hyperparameter_listOptimized hyperparameter values
infer_supporting_datasourcesGet the data sources that support the specific interactions...
ligand_activity_performance_top_i_removedCalculate ligand activity performance without considering...
lr_networkLigand-receptor network
make_discrete_ligand_target_matrixConvert probabilistic ligand-target matrix to a discrete one.
make_heatmap_bidir_lt_ggplotMake a ggplot heatmap object from an input ligand-target...
make_heatmap_ggplotMake a ggplot heatmap object from an input matrix (2-color).
make_threecolor_heatmap_ggplotMake a ggplot heatmap object from an input matrix (3-color).
mlrmbo_optimizationOptimization of objective functions via model-based...
model_based_ligand_activity_predictionPrediction of ligand activity prediction by a model trained...
model_evaluation_hyperparameter_optimizationConstruct and evaluate a ligand-target model given input...
model_evaluation_optimizationConstruct and evaluate a ligand-target model given input...
model_evaluation_optimization_applicationConstruct and evaluate a ligand-target model given input...
ncitationsNumber of citations for genes
nichenetrnichenetr: Linking Extracellular Protein Signals to Target...
normalize_single_cell_ligand_activitiesNormalize single-cell ligand activities
optimized_source_weights_dfOptimized data source weights
predict_ligand_activitiesPredict activities of ligands in regulating expression of a...
predict_single_cell_ligand_activitiesSingle-cell ligand activity prediction
prepare_ligand_target_visualizationPrepare heatmap visualization of the ligand-target links...
prepare_settings_leave_one_in_characterizationPrepare settings for leave-one-in characterization
prepare_settings_leave_one_out_characterizationPrepare settings for leave-one-out characterization
prepare_settings_one_vs_one_characterizationPrepare settings for one-vs-one characterization
process_characterization_ligand_predictionProcess the output of model evaluation for data source...
process_characterization_ligand_prediction_single_measuresProcess the output of model evaluation for data source...
process_characterization_popularity_slopes_ligand_predictionProcess the output of model evaluation for data source...
process_characterization_popularity_slopes_target_predictionProcess the output of model evaluation for data source...
process_characterization_target_predictionProcess the output of model evaluation for data source...
process_characterization_target_prediction_averageProcess the output of model evaluation for data source...
process_mlrmbo_nichenet_optimizationProcess the output of mlrmbo multi-objective optimization to...
randomize_complete_network_source_specificRandomize an integrated network by shuffling its source...
randomize_datasource_networkRandomize a network of a particular data source.
randomize_networkRandomize a network
scale_quantileCut off outer quantiles and rescale to a [0, 1] range
scaling_modified_zscoreNormalize values in a vector by the modified z-score method.
scaling_zscoreNormalize values in a vector by the z-score method
sig_networkSignaling network
single_ligand_activity_score_classificationAssess how well cells' ligand activities predict a binary...
single_ligand_activity_score_regressionPerform a correlation and regression analysis between cells'...
source_weights_dfData source weights
wrapper_average_performancesCalculate average performance of datasets of a specific...
wrapper_evaluate_single_importances_ligand_predictionEvaluation of ligand activity prediction performance of...
saeyslab/nichenetr documentation built on Aug. 31, 2019, 6:48 a.m.