Index

A

acronym() (Project property) activate_upload_form() (in module src.report_manager.index) add_basic_layout() (BasicApp method) add_configuration_to_report() (Dataset method) add_to_layout() (BasicApp method) addUniProtTexts() (in module src.graphdb_builder.databases.parsers.uniprotParser) Analysis (class in src.analytics_core.analytics_factory) analysis_queries() (Dataset property) analysis_type() (Analysis property)

angle_between() (in module src.analytics_core.analytics.analytics) append_data_type() (Project method) append_to_list() (in module src.analytics_core.utils) apply_pvalue_correction() (in module src.analytics_core.analytics.analytics) apply_pvalue_fdrcorrection() (in module src.analytics_core.analytics.analytics) apply_pvalue_permutation_fdrcorrection() (in module src.analytics_core.analytics.analytics) apply_pvalue_twostage_fdrcorrection() (in module src.analytics_core.analytics.analytics) archiveImportDirectory() (in module src.graphdb_builder.builder.loader) args() (Analysis property)

B

BasicApp (class in src.report_manager.apps.basicApp) batch_iterator() (in module src.graphdb_builder.builder_utils) build_drug_entity() (in module src.graphdb_builder.databases.parsers.drugBankParser) build_DrugBank_dictionary() (in module src.graphdb_builder.databases.parsers.drugBankParser) build_header() (ProjectApp method) build_HMDB_dictionary() (in module src.graphdb_builder.databases.parsers.hmdbParser) build_metabolite_entity() (in module src.graphdb_builder.databases.parsers.hmdbParser) build_network() (in module src.analytics_core.analytics.wgcnaAnalysis) build_page() (BasicApp method) (ProjectApp method)

build_project() (Project method) build_relationships_from_DrugBank() (in module src.graphdb_builder.databases.parsers.drugBankParser) build_relationships_from_HMDB() (in module src.graphdb_builder.databases.parsers.hmdbParser) buildMappingFromOBO() (in module src.graphdb_builder.mapping) buildPage() (DataUploadApp method) (HomePageApp method) (ImportsApp method) (LoginApp method) (ProjectCreationApp method) buildStats() (in module src.graphdb_builder.builder_utils)

C

calculate_anova() (in module src.analytics_core.analytics.analytics) calculate_anova_samr() (in module src.analytics_core.analytics.analytics) calculate_coefficient_variation() (in module src.analytics_core.analytics.analytics) calculate_correlations() (in module src.analytics_core.analytics.analytics) calculate_dabest() (in module src.analytics_core.analytics.analytics) calculate_discriminant_lines() (in module src.analytics_core.analytics.analytics) calculate_FeatureTraitSignificance() (in module src.analytics_core.analytics.wgcnaAnalysis) calculate_fold_change() (in module src.analytics_core.analytics.analytics) calculate_median_replicates() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) calculate_module_eigengenes() (in module src.analytics_core.analytics.wgcnaAnalysis) calculate_ModuleMembership() (in module src.analytics_core.analytics.wgcnaAnalysis) calculate_ModuleTrait_correlation() (in module src.analytics_core.analytics.wgcnaAnalysis) calculate_pairwise_ttest() (in module src.analytics_core.analytics.analytics) calculate_pvalue_from_tstats() (in module src.analytics_core.analytics.analytics) calculate_repeated_measures_anova() (in module src.analytics_core.analytics.analytics) calculate_rm_correlation() (in module src.analytics_core.analytics.analytics) calculate_THSD() (in module src.analytics_core.analytics.analytics) calculate_ttest() (in module src.analytics_core.analytics.analytics) calculate_ttest_samr() (in module src.analytics_core.analytics.analytics) call_Rpackage() (in module src.analytics_core.R_wrapper) change_style() (in module src.report_manager.index) change_style_data_upload() (in module src.report_manager.index) check_columns() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) check_equal_variances() (in module src.analytics_core.analytics.analytics) check_external_ids_in_db() (in module src.report_manager.apps.dataUpload) check_if_node_exists() (in module src.graphdb_builder.users.users_controller) (in module src.report_manager.apps.projectCreation) check_is_paired() (in module src.analytics_core.analytics.analytics) check_minimum_configuration() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) check_normality() (in module src.analytics_core.analytics.analytics) check_report_exists() (Project method) check_samples_in_project() (in module src.report_manager.apps.dataUpload) checkDirectory() (in module src.ckg_utils) (in module src.graphdb_builder.builder_utils) clinical_parser() (in module src.graphdb_builder.experiments.parsers.clinicalParser) ClinicalDataset (class in src.report_manager.dataset)

ClinicalKnowledge (class in src.report_manager.knowledge) cohen_d() (in module src.analytics_core.analytics.analytics) colors() (Knowledge property) complement_posthoc() (in module src.analytics_core.analytics.analytics) compress_directory() (in module src.graphdb_builder.builder_utils) (in module src.report_manager.utils) configuration() (Dataset property) configuration_files() (Project property) (ProjectApp property) connectToDB() (in module src.graphdb_connector.connector) convert_bytes() (in module src.graphdb_builder.builder_utils) convert_dash_to_json() (in module src.ckg_utils) convert_html_to_dash() (in module src.analytics_core.utils) (in module src.report_manager.utils) convert_html_to_pdf() (in module src.report_manager.utils) convertOBOtoNet() (in module src.graphdb_builder.builder_utils) convertToEdgeList() (in module src.analytics_core.analytics.analytics) copy_file_to_destination() (in module src.report_manager.utils) copytree() (in module src.graphdb_builder.builder_utils) correct_pairwise_ttest() (in module src.analytics_core.analytics.analytics) create_db_user() (in module src.graphdb_builder.users.users_controller) create_experiment_internal_identifiers() (in module src.report_manager.apps.dataUpload) create_mapping_cols_clinical() (in module src.report_manager.apps.dataUpload) create_new_ansamples() (in module src.report_manager.apps.dataUpload) create_new_biosamples() (in module src.report_manager.apps.dataUpload) create_new_project() (in module src.report_manager.apps.projectCreation) create_new_subjects() (in module src.report_manager.apps.dataUpload) create_node() (in module src.graphdb_connector.connector) create_project() (in module src.report_manager.index) create_user() (in module src.graphdb_builder.builder.create_user) create_user_from_command_line() (in module src.graphdb_builder.builder.create_user) create_user_from_file() (in module src.graphdb_builder.builder.create_user) create_user_node() (in module src.graphdb_builder.builder.create_user) create_violinplot() (in module src.analytics_core.viz.viz) createEmptyStats() (in module src.graphdb_builder.builder.importer) cutreeDynamic() (in module src.analytics_core.analytics.wgcnaAnalysis)

D

data() (Analysis property) (Dataset property) (Knowledge property) data_types() (Project property) databasesImport() (in module src.graphdb_builder.builder.importer) Dataset (class in src.report_manager.dataset) dataset_type() (Dataset property) datasets() (Project property) DataUploadApp (class in src.report_manager.apps.dataUploadApp) default() (DictDFEncoder method) (NumpyEncoder method) default_color() (Knowledge property) define_samr_method() (in module src.analytics_core.analytics.analytics) Dendrogram (class in src.analytics_core.viz.Dendrogram)

description() (BasicApp property) (Project property) df_sort_by_dendrogram() (in module src.analytics_core.analytics.wgcnaAnalysis) DictDFEncoder (class in src.ckg_utils) display_page() (in module src.report_manager.index) DNAseqDataset (class in src.report_manager.dataset) download_from_ftp() (in module src.graphdb_builder.builder_utils) download_knowledge() (Project method) download_PRIDE_data() (in module src.graphdb_builder.builder_utils) download_project() (Project method) download_project_datasets() (Project method) download_project_report() (Project method) download_report() (Report method) downloadDB() (in module src.graphdb_builder.builder_utils) draw() (in module src.notebooks.development.vis)

E

empty_report() (Project method) entities() (Knowledge property) entries_to_remove() (in module src.graphdb_builder.ontologies.ontologies_controller) eta_squared() (in module src.analytics_core.analytics.analytics) expand_cols() (in module src.graphdb_builder.builder_utils) expand_groups() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) experimental_design_parser() (in module src.graphdb_builder.experiments.parsers.clinicalParser) experimentImport() (in module src.graphdb_builder.builder.importer) experimentsImport() (in module src.graphdb_builder.builder.importer) export_contents() (in module src.graphdb_builder.builder_utils) extend_layout() (BasicApp method) extract_analytical_sample_identifiers() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_analytical_samples_info() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_attributes() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_biological_sample_analytical_sample_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_sample_clinical_variables_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_sample_group_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_sample_subject_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_sample_timepoint_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_sample_tissue_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biological_samples_info() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biosample_analytical_sample_relationship_attributes() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_biosample_identifiers() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_configuration() (Dataset method) extract_drugs() (in module src.graphdb_builder.databases.parsers.drugBankParser) extract_metabolites() (in module src.graphdb_builder.databases.parsers.hmdbParser) extract_modification_protein_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser)

extract_number_missing() (in module src.analytics_core.analytics.analytics) extract_participant_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_peptide_protein_modification_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_peptide_protein_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_peptide_subject_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_peptides() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_percentage_missing() (in module src.analytics_core.analytics.analytics) extract_project_disease_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_project_info() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_project_intervention_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_project_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_project_subject_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_project_tissue_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_protein_modification_subject_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_protein_modifications_modification_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_protein_modifications_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_protein_protein_modification_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_protein_subject_rels() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_responsible_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_style() (in module src.report_manager.utils) extract_subject_disease_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_subject_identifiers() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_subject_intervention_rels() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extract_subject_replicates() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_subject_replicates_from_regex() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) extract_timepoints() (in module src.graphdb_builder.experiments.parsers.clinicalParser) extractWESRelationships() (in module src.graphdb_builder.experiments.parsers.wesParser)

F

file_size() (in module src.graphdb_builder.builder_utils) filter_df_by_cluster() (in module src.analytics_core.analytics.wgcnaAnalysis) find() (User method) find_node() (in module src.graphdb_connector.connector) find_queries_involving_nodes() (in module src.graphdb_connector.query_utils) find_queries_involving_relationships() (in module src.graphdb_connector.query_utils) flatten() (in module src.analytics_core.analytics.analytics) (in module src.graphdb_builder.builder_utils)

footer() (BasicApp property) force() (ProjectApp property) format_anova_table() (in module src.analytics_core.analytics.analytics) format_output() (in module src.graphdb_builder.databases.parsers.uniprotParser) from_dict() (Project method) from_json() (Project method) fullImport() (in module src.graphdb_builder.builder.importer) fullUpdate() (in module src.graphdb_builder.builder.loader)

G

generate_configuration_tree() (in module src.analytics_core.viz.viz) generate_cypher_nodes_list() (Knowledge method) generate_dataset() (ClinicalDataset method) (Dataset method) (DNAseqDataset method) (ProteomicsDataset method) (RNAseqDataset method) generate_dataset_imports() (in module src.graphdb_builder.experiments.experiments_controller) generate_graph_files() (in module src.graphdb_builder.experiments.experiments_controller) generate_graphFiles() (in module src.graphdb_builder.ontologies.ontologies_controller) generate_html() (in module src.analytics_core.utils) generate_knowledge() (ClinicalDataset method) (ClinicalKnowledge method) (Dataset method) (MultiOmicsDataset method) (MultiOmicsKnowledge method) (Project method) (ProjectKnowledge method) (ProteomicsDataset method) (ProteomicsKnowledge method) generate_knowledge_from_annotations() (Knowledge method) generate_knowledge_from_edgelist() (Knowledge method) generate_knowledge_from_queries() (Knowledge method) generate_knowledge_from_regulation() (Knowledge method) generate_knowledge_from_similarity() (Knowledge method) generate_knowledge_from_wgcna() (Knowledge method) generate_knowledge_graph() (Knowledge method) generate_overlap_plots() (Project method) generate_project_attributes_plot() (Project method) generate_project_info_report() (Project method) generate_project_similarity_plots() (Project method) generate_report() (Dataset method) (Knowledge method) (Project method) generate_report_url() (in module src.report_manager.index) generate_result() (Analysis method) generate_upload_zip() (in module src.report_manager.index) generateGraphFiles() (in module src.graphdb_builder.databases.databases_controller) GenerateGraphFiles() (in module src.graphdb_builder.users.users_controller) generateStatsDataFrame() (in module src.graphdb_builder.builder.importer) generator_to_dict() (in module src.analytics_core.utils) genreate_knowledge_from_correlation() (Knowledge method) get_2_venn_diagram() (in module src.analytics_core.viz.viz) get_barplot() (in module src.analytics_core.viz.viz) get_boxplot_grid() (in module src.analytics_core.viz.viz) get_clinical_measurements_ready() (in module src.analytics_core.analytics.analytics) get_clustergrammer_link() (in module src.analytics_core.utils) get_clustergrammer_plot() (in module src.analytics_core.viz.viz) get_clusters_elements() (in module src.analytics_core.analytics.wgcnaAnalysis) get_coefficient_variation() (in module src.analytics_core.analytics.analytics) get_color_dict() (Dendrogram method) get_complex_heatmapplot() (in module src.analytics_core.viz.viz) get_config() (in module src.graphdb_builder.builder_utils) get_configuration() (in module src.ckg_utils) (in module src.graphdb_builder.experiments.parsers.proteomicsParser) get_configuration_variable() (in module src.ckg_utils) get_counts_permutation_fdr() (in module src.analytics_core.analytics.analytics) get_cytoscape_network() (in module src.analytics_core.viz.viz) get_data() (in module src.analytics_core.analytics.wgcnaAnalysis) get_data_ready_for_km() (in module src.analytics_core.analytics.kaplan_meierAnalysis) get_data_upload_queries() (in module src.report_manager.apps.dataUpload) get_databases_entities_relationships() (in module src.report_manager.apps.imports) get_dataframe() (Dataset method) get_dataframes() (Dataset method) (MultiOmicsDataset method) get_dataset() (Project method) get_dataset_configuration() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) get_dataset_data_directory() (Dataset method) get_db_schema() (in module src.report_manager.apps.homepageStats) get_db_stats_data() (in module src.report_manager.apps.homepageStats) get_dendrogram() (in module src.analytics_core.analytics.wgcnaAnalysis) get_dendrogram_traces() (Dendrogram method) get_description() (in module src.graphdb_connector.query_utils) get_distplot() (in module src.analytics_core.viz.viz) get_downloads_directory() (Project method) get_dropdown_menu() (in module src.report_manager.apps.imports) get_EigengenesTrait_correlation() (in module src.analytics_core.analytics.wgcnaAnalysis) get_extra_entities_rels() (in module src.graphdb_builder.ontologies.ontologies_controller) get_extra_pairs() (in module src.graphdb_builder.builder_utils) get_facet_grid_plot() (in module src.analytics_core.viz.viz) get_FeaturesPerModule() (in module src.analytics_core.analytics.wgcnaAnalysis) get_files_by_pattern() (in module src.graphdb_builder.builder_utils) get_full_path_directories() (in module src.graphdb_builder.builder_utils) get_heatmap() (in module src.analytics_core.viz.wgcnaFigures) get_heatmapplot() (in module src.analytics_core.viz.viz) get_hex_colors() (in module src.analytics_core.utils) (in module src.report_manager.utils)

get_histogram() (in module src.analytics_core.viz.viz) get_HTML_description() (BasicApp method) get_HTML_subtitle() (BasicApp method) get_HTML_title() (BasicApp method) get_image() (in module src.report_manager.utils) get_imports_per_database_date() (in module src.report_manager.apps.imports) get_inactive_terms() (in module src.graphdb_builder.ontologies.parsers.snomedParser) get_km_plot() (in module src.analytics_core.viz.viz) get_km_results() (in module src.analytics_core.analytics.kaplan_meierAnalysis) get_knowledge_graph_plot() (Knowledge method) get_louvain_partitions() (in module src.analytics_core.analytics.analytics) get_mapping_analytical_samples() (in module src.graphdb_builder.mapping) get_markdown() (in module src.analytics_core.viz.viz) get_markdown_date() (in module src.report_manager.utils) get_max_permutations() (in module src.analytics_core.analytics.analytics) get_miss_values_df() (in module src.analytics_core.analytics.wgcnaAnalysis) get_module_color_annotation() (in module src.analytics_core.viz.wgcnaFigures) get_ModuleFeatures() (in module src.analytics_core.analytics.wgcnaAnalysis) get_multi_table() (in module src.analytics_core.viz.viz) get_network() (in module src.analytics_core.viz.viz) get_network_communities() (in module src.analytics_core.analytics.analytics) get_network_style() (in module src.analytics_core.viz.viz) get_new_analytical_sample_identifier() (in module src.report_manager.apps.dataUpload) get_new_biosample_identifier() (in module src.report_manager.apps.dataUpload) get_new_project_identifier() (in module src.report_manager.apps.projectCreation) get_new_subject_identifier() (in module src.report_manager.apps.dataUpload) get_new_user_identifier() (in module src.graphdb_builder.users.users_controller) get_nodes() (in module src.graphdb_connector.query_utils) get_notebook_network_pyvis() (in module src.analytics_core.viz.viz) get_notebook_network_web() (in module src.analytics_core.viz.viz) get_parallel_plot() (in module src.analytics_core.viz.viz) get_pca_plot() (in module src.analytics_core.viz.viz) get_percentiles_heatmap() (in module src.analytics_core.analytics.wgcnaAnalysis) get_pieplot() (in module src.analytics_core.viz.viz) get_plot() (Analysis method) (Report method) get_polar_plot() (in module src.analytics_core.viz.viz) get_project_creation_queries() (in module src.report_manager.apps.projectCreation) get_project_information() (in module src.report_manager.apps.dataUpload) get_project_params_from_url() (in module src.report_manager.index) get_projects_overlap() (Project method) get_proteomics_measurements_ready() (in module src.analytics_core.analytics.analytics) get_publications_abstracts() (in module src.analytics_core.analytics.analytics) get_queries() (in module src.ckg_utils) get_query() (in module src.graphdb_connector.query_utils) (in module src.report_manager.apps.homepageStats) get_ranking_plot() (in module src.analytics_core.viz.viz) get_ranking_with_markers() (in module src.analytics_core.analytics.analytics) get_relationships() (in module src.graphdb_connector.query_utils) get_report_directory() (Project method) get_rgb_colors() (in module src.analytics_core.utils) (in module src.report_manager.utils) get_sankey_plot() (in module src.analytics_core.viz.viz) get_scatterplot() (in module src.analytics_core.viz.viz) get_scatterplot_matrix() (in module src.analytics_core.viz.viz) get_similar_projects() (Project method) get_similarity_network() (Project method) get_similarity_network_style() (Project method) get_simple_scatterplot() (in module src.analytics_core.viz.viz) get_stats_data() (in module src.report_manager.apps.imports) get_STRING_mapping_url() (in module src.graphdb_builder.mapping) get_subject_number_in_project() (in module src.report_manager.apps.projectCreation) get_subjects_enrolled_in_project() (in module src.report_manager.apps.dataUpload) get_summary_data_matrix() (in module src.analytics_core.analytics.analytics) get_table() (in module src.analytics_core.viz.viz) get_totals_per_date() (in module src.report_manager.apps.imports) get_user_creation_queries() (in module src.graphdb_builder.users.users_controller) get_value_cols() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) get_violinplot() (in module src.analytics_core.viz.viz) get_volcanoplot() (in module src.analytics_core.viz.viz) get_WGCNAPlots() (in module src.analytics_core.viz.viz) get_wordcloud() (in module src.analytics_core.viz.viz) getCurrentTime() (in module src.graphdb_builder.builder_utils) getCursorData() (in module src.graphdb_connector.connector) getGraphDatabaseConnectionConfiguration() (in module src.graphdb_connector.connector) getMapperFigure() (in module src.analytics_core.viz.viz) getMappingForEntity() (in module src.graphdb_builder.mapping) getMappingFromDatabase() (in module src.graphdb_builder.mapping) getMappingFromOntology() (in module src.graphdb_builder.mapping) getMedlineAbstracts() (in module src.analytics_core.utils) (in module src.graphdb_builder.builder_utils) getMultipleMappingForEntity() (in module src.graphdb_builder.mapping) getNumberText() (in module src.report_manager.utils) getPlotTraces() (in module src.analytics_core.viz.viz) getStatsName() (in module src.graphdb_builder.builder.importer) getSTRINGMapping() (in module src.graphdb_builder.mapping) graph() (Knowledge property) group_data_based_on_marker() (in module src.analytics_core.analytics.kaplan_meierAnalysis)

H

hedges_g() (in module src.analytics_core.analytics.analytics) hex2rgb() (in module src.analytics_core.utils) (in module src.report_manager.utils)

HomePageApp (class in src.report_manager.apps.homepageApp)

I

id() (ProjectApp property) identifier() (Analysis property) (Dataset property) (Knowledge property) (Project property) (Report property) identify_module_colors() (in module src.analytics_core.analytics.wgcnaAnalysis) image_formatter() (in module src.report_manager.index)

ImportsApp (class in src.report_manager.apps.importsApp) imputation_KNN() (in module src.analytics_core.analytics.analytics) imputation_mixed_norm_KNN() (in module src.analytics_core.analytics.analytics) imputation_normal_distribution() (in module src.analytics_core.analytics.analytics) indicator() (in module src.report_manager.apps.homepageStats) InteractomicsDataset (class in src.report_manager.dataset) invert_dict() (in module src.analytics_core.viz.color_list) is_jsonable() (in module src.ckg_utils) is_number() (in module src.graphdb_builder.builder_utils)

J

json_network_to_gml() (in module src.analytics_core.utils)

json_network_to_networkx() (in module src.analytics_core.utils)

K

Knowledge (class in src.report_manager.knowledge)

knowledge() (Project property)

L

layout() (BasicApp property) linear_normalization() (in module src.analytics_core.analytics.analytics) list_dataframes() (Dataset method) list_datasets() (Project method) list_ftp_directory() (in module src.graphdb_builder.builder_utils) list_plots() (Report method) list_queries() (in module src.graphdb_connector.query_utils) listDirectoryFiles() (in module src.ckg_utils) (in module src.graphdb_builder.builder_utils) listDirectoryFolders() (in module src.ckg_utils) (in module src.graphdb_builder.builder_utils) listDirectoryFoldersNotEmpty() (in module src.graphdb_builder.builder_utils)

load_dataset() (Dataset method) (in module src.graphdb_builder.experiments.parsers.proteomicsParser) load_dataset_recursively() (Dataset method) load_dataset_report() (Dataset method) load_into_database() (in module src.graphdb_builder.builder.loader) load_project() (Project method) load_project_data() (Project method) load_project_report() (Project method) loadWESDataset() (in module src.graphdb_builder.experiments.parsers.wesParser) LoginApp (class in src.report_manager.apps.loginApp) logo() (BasicApp property) LongitudinalProteomicsDataset (class in src.report_manager.dataset)

M

make_color_dict() (in module src.analytics_core.viz.color_list) make_interactive() (Analysis method) map_experiment_files() (in module src.graphdb_builder.mapping) map_experimental_data() (in module src.graphdb_builder.mapping) map_node_name_to_id() (in module src.graphdb_connector.query_utils) mark_complete_mapping() (in module src.graphdb_builder.mapping) median_normalization() (in module src.analytics_core.analytics.analytics) median_polish_normalization() (in module src.analytics_core.analytics.analytics)

merge_col_attributes() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) merge_for_polar() (in module src.analytics_core.analytics.analytics) merge_regex_attributes() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) merge_similar_modules() (in module src.analytics_core.analytics.wgcnaAnalysis) modifyEntityProperty() (in module src.graphdb_connector.connector) most_central_edge() (in module src.analytics_core.analytics.analytics) mpl_to_plotly() (in module src.analytics_core.viz.viz) MultiOmicsDataset (class in src.report_manager.dataset) MultiOmicsKnowledge (class in src.report_manager.knowledge)

N

name() (Project property) neo4j_path_to_networkx() (in module src.analytics_core.utils) neo4j_schema_to_networkx() (in module src.analytics_core.utils) network_to_tables() (in module src.analytics_core.viz.viz) networkx_to_cytoscape() (in module src.analytics_core.utils) networkx_to_gml() (in module src.analytics_core.utils)

nodes() (Knowledge property) normalize_data() (in module src.analytics_core.analytics.analytics) normalize_data_per_group() (in module src.analytics_core.analytics.analytics) notify_project_ready() (Project method) num_subjects() (Project property) number_panel_update() (in module src.report_manager.index) NumpyEncoder (class in src.ckg_utils)

O

omega_squared() (in module src.analytics_core.analytics.analytics)

ontologiesImport() (in module src.graphdb_builder.builder.importer) overlap() (Project property)

P

page_type() (BasicApp property) parse_annotations_with_pandas() (in module src.graphdb_builder.databases.parsers.goaParser) parse_contents() (in module src.graphdb_builder.builder_utils) parse_dataset() (in module src.graphdb_builder.experiments.parsers.clinicalParser) (in module src.graphdb_builder.experiments.parsers.proteomicsParser) parse_fasta() (in module src.graphdb_builder.builder_utils) (in module src.graphdb_builder.databases.parsers.uniprotParser) parse_from_directory() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) parse_html() (in module src.analytics_core.utils) (in module src.report_manager.utils) parse_idmapping_file() (in module src.graphdb_builder.databases.parsers.uniprotParser) parse_mentions() (in module src.graphdb_builder.databases.parsers.textminingParser) parse_ontology() (in module src.graphdb_builder.ontologies.ontologies_controller) parse_PMC_list() (in module src.graphdb_builder.databases.parsers.textminingParser) parse_release_notes() (in module src.graphdb_builder.databases.parsers.uniprotParser) parse_standard_dataset() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) parse_substrates() (in module src.graphdb_builder.databases.parsers.signorParser) parseActions() (in module src.graphdb_builder.databases.parsers.stringParser) parseBiomarkersFile() (in module src.graphdb_builder.databases.parsers.exposomeParser) parseCompounds() (in module src.graphdb_builder.databases.parsers.foodbParser) parseContents() (in module src.graphdb_builder.databases.parsers.foodbParser) parseCorrelationsFile() (in module src.graphdb_builder.databases.parsers.exposomeParser) parseDatabase() (in module src.graphdb_builder.databases.databases_controller) parseDiseaseAnnotations() (in module src.graphdb_builder.databases.parsers.pspParser) parseDrugBankVocabulary() (in module src.graphdb_builder.databases.parsers.drugBankParser) parseFood() (in module src.graphdb_builder.databases.parsers.foodbParser) parseKinaseSubstrates() (in module src.graphdb_builder.databases.parsers.pspParser) parsePairs() (in module src.graphdb_builder.databases.parsers.jensenlabParser) parsePathologyFile() (in module src.graphdb_builder.databases.parsers.hpaParser) parsePathwayHierarchy() (in module src.graphdb_builder.databases.parsers.reactomeParser) parsePathwayMetaboliteDrugRelationships() (in module src.graphdb_builder.databases.parsers.smpdbParser) parsePathwayProteinRelationships() (in module src.graphdb_builder.databases.parsers.smpdbParser) parsePathwayRelationships() (in module src.graphdb_builder.databases.parsers.reactomeParser) parsePathways() (in module src.graphdb_builder.databases.parsers.reactomeParser) (in module src.graphdb_builder.databases.parsers.smpdbParser) parser() (in module src.graphdb_builder.databases.parsers.cancerGenomeInterpreterParser) (in module src.graphdb_builder.databases.parsers.corumParser) (in module src.graphdb_builder.databases.parsers.disgenetParser) (in module src.graphdb_builder.databases.parsers.drugBankParser) (in module src.graphdb_builder.databases.parsers.drugGeneInteractionDBParser) (in module src.graphdb_builder.databases.parsers.exposomeParser) (in module src.graphdb_builder.databases.parsers.foodbParser) (in module src.graphdb_builder.databases.parsers.goaParser) (in module src.graphdb_builder.databases.parsers.gwasCatalogParser) (in module src.graphdb_builder.databases.parsers.hgncParser) (in module src.graphdb_builder.databases.parsers.hmdbParser) (in module src.graphdb_builder.databases.parsers.hpaParser) (in module src.graphdb_builder.databases.parsers.intactParser) (in module src.graphdb_builder.databases.parsers.jensenlabParser) (in module src.graphdb_builder.databases.parsers.mutationDsParser) (in module src.graphdb_builder.databases.parsers.oncokbParser) (in module src.graphdb_builder.databases.parsers.pathwayCommonsParser) (in module src.graphdb_builder.databases.parsers.pfamParser) (in module src.graphdb_builder.databases.parsers.pspParser) (in module src.graphdb_builder.databases.parsers.reactomeParser) (in module src.graphdb_builder.databases.parsers.refseqParser) (in module src.graphdb_builder.databases.parsers.siderParser) (in module src.graphdb_builder.databases.parsers.signorParser) (in module src.graphdb_builder.databases.parsers.smpdbParser) (in module src.graphdb_builder.databases.parsers.stringParser) (in module src.graphdb_builder.databases.parsers.textminingParser) (in module src.graphdb_builder.databases.parsers.uniprotParser) (in module src.graphdb_builder.experiments.parsers.clinicalParser) (in module src.graphdb_builder.experiments.parsers.proteomicsParser) (in module src.graphdb_builder.experiments.parsers.wesParser) (in module src.graphdb_builder.ontologies.parsers.efoParser) (in module src.graphdb_builder.ontologies.parsers.icdParser) (in module src.graphdb_builder.ontologies.parsers.oboParser) (in module src.graphdb_builder.ontologies.parsers.reflectParser) (in module src.graphdb_builder.ontologies.parsers.snomedParser)

parser_from_file() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) parseRegulationAnnotations() (in module src.graphdb_builder.databases.parsers.pspParser) parserIndications() (in module src.graphdb_builder.databases.parsers.siderParser) parseSites() (in module src.graphdb_builder.databases.parsers.pspParser) parseUniProtAnnotations() (in module src.graphdb_builder.databases.parsers.uniprotParser) parseUniProtPeptides() (in module src.graphdb_builder.databases.parsers.uniprotParser) parseUniProtVariants() (in module src.graphdb_builder.databases.parsers.uniprotParser) parseUsersFile() (in module src.graphdb_builder.users.users_controller) parseWESDataset() (in module src.graphdb_builder.experiments.parsers.wesParser) partialUpdate() (in module src.graphdb_builder.builder.loader) paste_matrices() (in module src.analytics_core.analytics.wgcnaAnalysis) PhosphoproteomicsDataset (class in src.report_manager.dataset) pick_softThreshold() (in module src.analytics_core.analytics.wgcnaAnalysis) plot() (Analysis property) plot_2_venn_diagram() (in module src.analytics_core.viz.viz) plot_complex_dendrogram() (in module src.analytics_core.viz.wgcnaFigures) plot_databases_numbers_per_date() (in module src.report_manager.apps.imports) plot_dendrogram() (in module src.analytics_core.viz.Dendrogram) plot_dendrogram_guidelines() (in module src.analytics_core.viz.wgcnaFigures) plot_import_numbers_per_database() (in module src.report_manager.apps.imports) plot_intramodular_correlation() (in module src.analytics_core.viz.wgcnaFigures) plot_labeled_heatmap() (in module src.analytics_core.viz.wgcnaFigures) plot_node_rel_per_label() (in module src.report_manager.apps.homepageStats) plot_store_size_components() (in module src.report_manager.apps.homepageStats) plot_total_number_imported() (in module src.report_manager.apps.imports) plot_total_numbers_per_date() (in module src.report_manager.apps.imports) plots() (Analysis property) (Report property) pretty_print() (in module src.graphdb_builder.builder_utils) print_files() (in module src.graphdb_builder.databases.parsers.pfamParser) print_multiple_relationships_files() (in module src.graphdb_builder.databases.parsers.uniprotParser) print_report() (Report method) print_single_file() (in module src.graphdb_builder.databases.parsers.uniprotParser) process_dataset() (ClinicalDataset method) (ProteomicsDataset method) processing() (ClinicalDataset method) (ProteomicsDataset method) Project (class in src.report_manager.project) project_id() (ProjectApp property) project_parser() (in module src.graphdb_builder.experiments.parsers.clinicalParser) ProjectApp (class in src.report_manager.apps.projectApp) ProjectCreationApp (class in src.report_manager.apps.projectCreationApp) ProjectKnowledge (class in src.report_manager.knowledge) ProteomicsDataset (class in src.report_manager.dataset) ProteomicsKnowledge (class in src.report_manager.knowledge) PTMDataset (class in src.report_manager.dataset) publish_analysis() (Analysis method)

Q

quantile_normalization() (in module src.analytics_core.analytics.analytics) queries_file() (Knowledge property) (Project property)

query_data() (Dataset method) (Knowledge method) (Project method) quick_numbers_panel() (in module src.report_manager.apps.homepageStats)

R

R_matrix2Py_matrix() (in module src.analytics_core.R_wrapper) read_colors() (in module src.analytics_core.viz.color_list) read_gzipped_file() (in module src.graphdb_builder.builder_utils) read_knowledge_queries() (in module src.graphdb_connector.query_utils) read_queries() (in module src.graphdb_connector.query_utils) read_report() (Report method) read_valid_pubs() (in module src.graphdb_builder.databases.parsers.textminingParser) read_yaml() (in module src.ckg_utils) readDataFromCSV() (in module src.graphdb_builder.builder_utils) readDataFromExcel() (in module src.graphdb_builder.builder_utils) readDataFromTXT() (in module src.graphdb_builder.builder_utils) readDataset() (in module src.graphdb_builder.builder_utils) readDisGeNetDiseaseMapping() (in module src.graphdb_builder.databases.parsers.disgenetParser) readDisGeNetProteinMapping() (in module src.graphdb_builder.databases.parsers.disgenetParser) reduce_to_subgraph() (Knowledge method) regenerate_report() (in module src.report_manager.index) register() (User method) relationships() (Knowledge property) remove_contaminant_tag() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) remove_directory() (in module src.graphdb_builder.builder_utils) remove_group() (in module src.analytics_core.analytics.analytics) remove_legend_duplicates() (in module src.report_manager.apps.imports) remove_project() (Project method) remove_samples_nodes_db() (in module src.report_manager.apps.dataUpload) removeRelationshipDB() (in module src.graphdb_connector.connector) Report (class in src.report_manager.report) report() (Dataset property) (Knowledge property) (Project property) reset_mapping() (in module src.graphdb_builder.mapping) responsible() (Project property) result() (Analysis property)

return_docs() (in module src.report_manager.index) RNAseqDataset (class in src.report_manager.dataset) route_login() (in module src.report_manager.index) route_logout() (in module src.report_manager.index) route_report_url() (in module src.report_manager.index) route_upload_url() (in module src.report_manager.index) run_anova() (in module src.analytics_core.analytics.analytics) run_correlation() (in module src.analytics_core.analytics.analytics) run_dabest() (in module src.analytics_core.analytics.analytics) run_efficient_correlation() (in module src.analytics_core.analytics.analytics) run_enrichment() (in module src.analytics_core.analytics.analytics) run_fisher() (in module src.analytics_core.analytics.analytics) run_km() (in module src.analytics_core.analytics.analytics) (in module src.analytics_core.analytics.kaplan_meierAnalysis) run_kolmogorov_smirnov() (in module src.analytics_core.analytics.analytics) run_mapper() (in module src.analytics_core.analytics.analytics) run_multi_correlation() (in module src.analytics_core.analytics.analytics) run_pca() (in module src.analytics_core.analytics.analytics) run_processing() (in module src.report_manager.index) run_qc_markers_analysis() (in module src.analytics_core.analytics.analytics) run_regulation_enrichment() (in module src.analytics_core.analytics.analytics) run_repeated_measurements_anova() (in module src.analytics_core.analytics.analytics) run_rm_correlation() (in module src.analytics_core.analytics.analytics) run_samr() (in module src.analytics_core.analytics.analytics) run_site_regulation_enrichment() (in module src.analytics_core.analytics.analytics) run_snf() (in module src.analytics_core.analytics.analytics) run_tsne() (in module src.analytics_core.analytics.analytics) run_ttest() (in module src.analytics_core.analytics.analytics) run_two_way_anova() (in module src.analytics_core.analytics.analytics) run_umap() (in module src.analytics_core.analytics.analytics) run_volcano() (in module src.analytics_core.viz.viz) run_WGCNA() (in module src.analytics_core.analytics.analytics)

S

save_analysis_plots() (Analysis method) save_analysis_result() (Analysis method) save_DASH_plot() (in module src.analytics_core.viz.viz) save_dataset() (Dataset method) save_dataset_recursively() (Dataset method) save_dataset_recursively_to_file() (Dataset method) save_dataset_to_file() (Dataset method) save_dict_to_yaml() (in module src.ckg_utils) save_files_in_tmp() (in module src.report_manager.index) save_project() (Project method) save_project_datasets_data() (Project method) save_project_datasets_reports() (Project method) save_project_report() (Project method) save_report() (Dataset method) (Knowledge method) (Report method) searchPubmed() (in module src.graphdb_builder.builder_utils) select_last_n_imports() (in module src.report_manager.apps.imports) send_email() (in module src.report_manager.utils) send_message_to_slack_webhook() (in module src.report_manager.utils) send_query() (Dataset method) (Knowledge method) sendQuery() (in module src.graphdb_connector.connector) serve_static() (in module src.report_manager.index) session_id() (ProjectApp property) set_arguments() (in module src.graphdb_builder.builder.builder) (in module src.graphdb_builder.builder.create_user) set_attributes() (Project method) set_axis_layout() (Dendrogram method) set_colors() (in module src.report_manager.apps.imports) set_configuration_from_file() (Dataset method) set_figure_layout() (Dendrogram method) setup_config() (in module src.graphdb_builder.builder_utils) setup_logging() (in module src.ckg_utils) (in module src.graphdb_builder.builder_utils) setupStats() (in module src.graphdb_builder.builder.importer) show_proteomics_file_options() (in module src.report_manager.index) show_proteomics_options() (in module src.report_manager.index) show_report() (Project method) similar_projects() (Project property) size_converter() (in module src.report_manager.apps.homepageStats) src.analytics_core.analytics.analytics (module) src.analytics_core.analytics.kaplan_meierAnalysis (module) src.analytics_core.analytics.wgcnaAnalysis (module) src.analytics_core.analytics_factory (module) src.analytics_core.R_wrapper (module) src.analytics_core.utils (module) src.analytics_core.viz.color_list (module) src.analytics_core.viz.Dendrogram (module) src.analytics_core.viz.viz (module) src.analytics_core.viz.wgcnaFigures (module) src.ckg_utils (module) src.graphdb_builder.builder.builder (module) src.graphdb_builder.builder.create_user (module) src.graphdb_builder.builder.importer (module) src.graphdb_builder.builder.loader (module) src.graphdb_builder.builder_utils (module) src.graphdb_builder.databases.databases_controller (module) src.graphdb_builder.databases.parsers.cancerGenomeInterpreterParser (module) src.graphdb_builder.databases.parsers.corumParser (module) src.graphdb_builder.databases.parsers.disgenetParser (module)

src.graphdb_builder.databases.parsers.drugBankParser (module) src.graphdb_builder.databases.parsers.drugGeneInteractionDBParser (module) src.graphdb_builder.databases.parsers.exposomeParser (module) src.graphdb_builder.databases.parsers.foodbParser (module) src.graphdb_builder.databases.parsers.goaParser (module) src.graphdb_builder.databases.parsers.gwasCatalogParser (module) src.graphdb_builder.databases.parsers.hgncParser (module) src.graphdb_builder.databases.parsers.hmdbParser (module) src.graphdb_builder.databases.parsers.hpaParser (module) src.graphdb_builder.databases.parsers.intactParser (module) src.graphdb_builder.databases.parsers.jensenlabParser (module) src.graphdb_builder.databases.parsers.mutationDsParser (module) src.graphdb_builder.databases.parsers.oncokbParser (module) src.graphdb_builder.databases.parsers.pathwayCommonsParser (module) src.graphdb_builder.databases.parsers.pfamParser (module) src.graphdb_builder.databases.parsers.pspParser (module) src.graphdb_builder.databases.parsers.reactomeParser (module) src.graphdb_builder.databases.parsers.refseqParser (module) src.graphdb_builder.databases.parsers.siderParser (module) src.graphdb_builder.databases.parsers.signorParser (module) src.graphdb_builder.databases.parsers.smpdbParser (module) src.graphdb_builder.databases.parsers.stringParser (module) src.graphdb_builder.databases.parsers.textminingParser (module) src.graphdb_builder.databases.parsers.uniprotParser (module) src.graphdb_builder.experiments.experiments_controller (module) src.graphdb_builder.experiments.parsers.clinicalParser (module) src.graphdb_builder.experiments.parsers.proteomicsParser (module) src.graphdb_builder.experiments.parsers.wesParser (module) src.graphdb_builder.mapping (module) src.graphdb_builder.ontologies.ontologies_controller (module) src.graphdb_builder.ontologies.parsers.efoParser (module) src.graphdb_builder.ontologies.parsers.icdParser (module) src.graphdb_builder.ontologies.parsers.oboParser (module) src.graphdb_builder.ontologies.parsers.reflectParser (module) src.graphdb_builder.ontologies.parsers.snomedParser (module) src.graphdb_builder.users.users_controller (module) src.graphdb_connector.connector (module) src.graphdb_connector.query_utils (module) src.notebooks.development.vis (module) src.report_manager.app (module) src.report_manager.apps.basicApp (module) src.report_manager.apps.dataUpload (module) src.report_manager.apps.dataUploadApp (module) src.report_manager.apps.homepageApp (module) src.report_manager.apps.homepageStats (module) src.report_manager.apps.imports (module) src.report_manager.apps.importsApp (module) src.report_manager.apps.initialApp (module) src.report_manager.apps.loginApp (module) src.report_manager.apps.projectApp (module) src.report_manager.apps.projectCreation (module) src.report_manager.apps.projectCreationApp (module) src.report_manager.dataset (module) src.report_manager.index (module) src.report_manager.knowledge (module) src.report_manager.project (module) src.report_manager.report (module) src.report_manager.user (module) src.report_manager.utils (module) src.report_manager.worker (module) status() (Project property) subtitle() (BasicApp property)

T

title() (BasicApp property) to_dataframe() (Project method) to_dict() (Project method)

to_json() (Project method) transform_into_long_format() (in module src.analytics_core.analytics.analytics) transform_into_wide_format() (in module src.analytics_core.analytics.analytics) transform_proteomics_edgelist() (in module src.analytics_core.analytics.analytics)

U

unit_vector() (in module src.analytics_core.analytics.analytics) unrar() (in module src.graphdb_builder.builder_utils) update_analysis_queries() (Dataset method) update_configuration() (in module src.graphdb_builder.experiments.parsers.proteomicsParser) update_configuration_from_file() (Dataset method) update_data() (Dataset method) update_dataset() (Project method) update_db_date() (in module src.report_manager.index) update_download_link() (in module src.report_manager.index) update_groups() (in module src.graphdb_builder.experiments.parsers.proteomicsParser)

update_nodes() (Knowledge method) update_output() (in module src.report_manager.index) update_plots() (Analysis method) (Report method) update_project_url() (in module src.report_manager.index) update_relationships() (Knowledge method) update_report() (Dataset method) (Project method) updateDB() (in module src.graphdb_builder.builder.loader) User (class in src.report_manager.user) usersImport() (in module src.graphdb_builder.builder.importer)

V

verify_password() (User method) vis_network() (in module src.notebooks.development.vis) visualize_notebook_network() (in module src.analytics_core.viz.viz)

visualize_notebook_path() (in module src.analytics_core.viz.viz) visualize_plot() (Report method) visualize_report() (Report method)

W

widen_original_dataset() (ClinicalDataset method) write_entities() (in module src.graphdb_builder.builder_utils)

write_relationships() (in module src.graphdb_builder.builder_utils) writeStats() (in module src.graphdb_builder.builder.importer)

Z

zscore_normalization() (in module src.analytics_core.analytics.analytics)