├── .dockerignore ├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── Dockerfile ├── Docs ├── RESULTS-DOCUMENTATION.md ├── cluster_statistical_analysis_method_workflow.md ├── create_datafiles.md ├── database.md ├── deploying.md ├── images │ ├── cluster_statistical_analysis_launcher.png │ ├── cluster_statistical_analysis_workflow.png │ ├── cluster_statistical_complex_method_workflow.png │ ├── database-schema.png │ ├── project_workflow.png │ └── statistical_analysis.png ├── ppi-resources.md ├── project_structure.md └── project_workflow.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── cellphonedb.ini ├── cellphonedb ├── __init__.py ├── cellphonedb_cli.py ├── src │ ├── __init__.py │ ├── api_endpoints │ │ ├── __init__.py │ │ ├── terminal_api │ │ │ ├── __init__.py │ │ │ ├── database_terminal_api_endpoints │ │ │ │ ├── __init__.py │ │ │ │ └── database_terminal_commands.py │ │ │ ├── method_terminal_api_endpoints │ │ │ │ ├── __init__.py │ │ │ │ └── method_terminal_commands.py │ │ │ ├── plot_terminal_api_endpoints │ │ │ │ ├── __init__.py │ │ │ │ └── plot_terminal_commands.py │ │ │ ├── query_terminal_api_endpoints │ │ │ │ ├── __init__.py │ │ │ │ └── query_terminal_commands.py │ │ │ ├── tools_terminal_api_endpoints │ │ │ │ ├── __init__.py │ │ │ │ └── tools_terminal_commands.py │ │ │ └── util │ │ │ │ ├── __init__.py │ │ │ │ └── choose_database.py │ │ └── web_api │ │ │ ├── __init__.py │ │ │ ├── query_web_api_endpoints │ │ │ ├── __init__.py │ │ │ ├── complex │ │ │ │ ├── __init__.py │ │ │ │ ├── query_complex_web_api_routes.py │ │ │ │ └── web_endpoint_query_complex_deconvoluted.py │ │ │ ├── interaction │ │ │ │ ├── __init__.py │ │ │ │ ├── query_interaction_web_api_routes.py │ │ │ │ └── web_endpoint_query_interaction_gene.py │ │ │ ├── query_web_api_routes.py │ │ │ ├── web_endpoint_query_autocomplete.py │ │ │ ├── web_endpoint_query_database.py │ │ │ └── web_endpoint_query_find_interactions_by_element.py │ │ │ ├── routes.py │ │ │ └── web_api_endpoint_base.py │ ├── app │ │ ├── __init__.py │ │ ├── app_config.py │ │ ├── app_logger.py │ │ ├── cellphonedb_app.py │ │ ├── config │ │ │ ├── base_config.yml │ │ │ ├── core.yml │ │ │ ├── docker_test.yml │ │ │ ├── postgres_local.yml │ │ │ └── test.yml │ │ ├── cpdb_app.py │ │ └── flask │ │ │ ├── __init__.py │ │ │ ├── flask_app.py │ │ │ └── flask_cellphonedb.py │ ├── core │ │ ├── Cellphonedb.py │ │ ├── CellphonedbSqlalchemy.py │ │ ├── __init__.py │ │ ├── cellphone.db │ │ ├── collectors │ │ │ ├── __init__.py │ │ │ ├── collector.py │ │ │ ├── complex_preprocess_collector.py │ │ │ ├── gene_preprocess_collector.py │ │ │ ├── interaction_preprocess_collector.py │ │ │ └── protein_preprocess_collector.py │ │ ├── core_logger.py │ │ ├── data │ │ │ ├── complex_input.csv │ │ │ ├── gene_input.csv │ │ │ ├── interaction_input.csv │ │ │ ├── protein_input.csv │ │ │ └── sources │ │ │ │ ├── I2D_interaction_raw.csv.xz │ │ │ │ ├── IMEx_interaction_raw.csv.xz │ │ │ │ ├── InnateDB-All_interaction_raw.csv.xz │ │ │ │ ├── InnateDB_interaction_raw.csv.xz │ │ │ │ ├── IntAct_interaction_raw.csv.xz │ │ │ │ ├── MBInfo_interaction_raw.csv.xz │ │ │ │ ├── MINT_interaction_raw.csv.xz │ │ │ │ ├── MatrixDB_interaction_raw.csv.xz │ │ │ │ ├── UniProt_interaction_raw.csv.xz │ │ │ │ ├── bhf-ucl_interaction_raw.csv.xz │ │ │ │ ├── complex_curated.csv │ │ │ │ ├── ensembl.txt │ │ │ │ ├── excluded_interaction.csv │ │ │ │ ├── hla_curated.csv │ │ │ │ ├── interaction_curated.csv │ │ │ │ ├── iuphar_interaction_raw.csv.xz │ │ │ │ ├── protein_curated.csv │ │ │ │ └── uniprot.tab │ │ ├── database │ │ │ ├── Database.py │ │ │ ├── DatabaseManager.py │ │ │ ├── Repository.py │ │ │ ├── __init__.py │ │ │ ├── sqlalchemy_models │ │ │ │ ├── __init__.py │ │ │ │ ├── db_model_complex.py │ │ │ │ ├── db_model_complex_composition.py │ │ │ │ ├── db_model_gene.py │ │ │ │ ├── db_model_interaction.py │ │ │ │ ├── db_model_multidata.py │ │ │ │ └── db_model_protein.py │ │ │ └── sqlalchemy_repository │ │ │ │ ├── ComplexRepository.py │ │ │ │ ├── GeneRepository.py │ │ │ │ ├── InteractionRepository.py │ │ │ │ ├── MultidataRepository.py │ │ │ │ ├── ProteinRepository.py │ │ │ │ └── __init__.py │ │ ├── exceptions │ │ │ ├── AllCountsFilteredException.py │ │ │ ├── EmptyResultException.py │ │ │ ├── NoComplexException.py │ │ │ ├── NoInteractionsFound.py │ │ │ ├── ProcessMetaException.py │ │ │ ├── ThresholdValueException.py │ │ │ └── __init__.py │ │ ├── exporters │ │ │ ├── __init__.py │ │ │ ├── complex_exporter.py │ │ │ ├── exporterlauncher.py │ │ │ ├── gene_exporter.py │ │ │ ├── interaction_exporter.py │ │ │ ├── protein_complex_cellphonedb.py │ │ │ └── protein_exporter.py │ │ ├── generators │ │ │ ├── __init__.py │ │ │ ├── complex_generator.py │ │ │ ├── gene_generator.py │ │ │ ├── generator_helper.py │ │ │ └── protein_generator.py │ │ ├── metadata.json │ │ ├── methods │ │ │ ├── __init__.py │ │ │ ├── cpdb_analysis_complex_method.py │ │ │ ├── cpdb_analysis_helper.py │ │ │ ├── cpdb_analysis_method.py │ │ │ ├── cpdb_statistical_analysis_complex_method.py │ │ │ ├── cpdb_statistical_analysis_helper.py │ │ │ ├── cpdb_statistical_analysis_method.py │ │ │ ├── method_launcher.py │ │ │ └── method_utils.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── cluster_counts │ │ │ │ ├── __init__.py │ │ │ │ ├── cluster_counts_filter.py │ │ │ │ └── cluster_counts_helper.py │ │ │ ├── complex │ │ │ │ ├── __init__.py │ │ │ │ └── complex_helper.py │ │ │ ├── interaction │ │ │ │ ├── __init__.py │ │ │ │ ├── interaction_filter.py │ │ │ │ ├── interaction_helper.py │ │ │ │ └── interaction_properties.py │ │ │ └── multidata │ │ │ │ ├── __init__.py │ │ │ │ ├── multidata_helper.py │ │ │ │ └── multidata_properties.py │ │ ├── preprocessors │ │ │ ├── __init__.py │ │ │ └── method_preprocessors.py │ │ ├── queries │ │ │ ├── __init__.py │ │ │ ├── autocomplete_queries.py │ │ │ ├── complex │ │ │ │ ├── __init__.py │ │ │ │ └── complex_deconvoluted.py │ │ │ ├── interaction │ │ │ │ ├── __init__.py │ │ │ │ └── interactions_by_element.py │ │ │ └── query_launcher.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── fixtures │ │ │ │ ├── cluster_counts_model │ │ │ │ │ ├── cluster_counts_filter_empty_cluster_results.csv │ │ │ │ │ ├── cluster_counts_generic_cluster_counts.csv │ │ │ │ │ ├── cluster_counts_helper_get_complex_involved_in_counts_result.csv │ │ │ │ │ ├── cluster_counts_helper_merge_complex_cluster_counts_complex_counts_composition.csv │ │ │ │ │ ├── cluster_counts_helper_merge_complex_cluster_counts_result.csv │ │ │ │ │ ├── cluster_counts_helper_threshold_results.csv │ │ │ │ │ ├── helper_cluster_counts.csv │ │ │ │ │ ├── helper_cluster_counts_complex.csv │ │ │ │ │ └── helper_cluster_counts_complex_composition.csv │ │ │ │ ├── filter_interaction │ │ │ │ │ ├── filter_interaction_integrin_proteins.csv │ │ │ │ │ ├── filter_interaction_interactions.csv │ │ │ │ │ ├── filter_interaction_interactions_filtered.csv │ │ │ │ │ ├── filter_interaction_multidatas_interaction.csv │ │ │ │ │ └── filter_interaction_multidatas_multidata.csv │ │ │ │ ├── helper_complex │ │ │ │ │ ├── helper_complex_complex.csv │ │ │ │ │ ├── helper_complex_complex_composition.csv │ │ │ │ │ ├── helper_complex_protein.csv │ │ │ │ │ ├── helper_complex_result.csv │ │ │ │ │ └── helper_complex_result_drop_duplicates.csv │ │ │ │ ├── preprocessors_fixtures │ │ │ │ │ ├── meta_multiple_columns_all_defined.txt │ │ │ │ │ ├── meta_multiple_columns_celltype_defined.txt │ │ │ │ │ ├── meta_multiple_columns_miss_multiple_header_fail.txt │ │ │ │ │ ├── meta_multiple_columns_miss_one_header.txt │ │ │ │ │ ├── meta_multiple_columns_one_incomplete_header.txt │ │ │ │ │ ├── meta_multiple_columns_random_uppercase.txt │ │ │ │ │ ├── meta_one_column_fail.txt │ │ │ │ │ ├── meta_result_preprocessor.txt │ │ │ │ │ ├── meta_two_columns_both_defined.txt │ │ │ │ │ ├── meta_two_columns_none_defined.txt │ │ │ │ │ └── meta_wrong_format_fail.txt │ │ │ │ ├── real_cells_to_clusters.csv │ │ │ │ └── real_cells_to_clusters_result.csv │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── cluster_counts │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── test_filter_cluster_counts.py │ │ │ │ ├── test_helper_complex.py │ │ │ │ ├── test_interaction_filters.py │ │ │ │ └── test_properties_multidata.py │ │ │ ├── preprocessors_tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_method_preprocessors.py │ │ │ └── queries │ │ │ │ ├── __init__.py │ │ │ │ └── test_autocomplete_queries.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── filters.py │ │ │ └── subsampler.py │ ├── database │ │ ├── __init__.py │ │ └── manager │ │ │ ├── DatabaseVersionManager.py │ │ │ └── __init__.py │ ├── exceptions │ │ ├── MissingPlotterFunctionException.py │ │ ├── MissingR.py │ │ ├── MissingRequiredColumns.py │ │ ├── NoReleasesException.py │ │ ├── NotADataFrameException.py │ │ ├── ParseCountsException.py │ │ ├── ParseMetaException.py │ │ ├── PlotException.py │ │ ├── RRuntimeException.py │ │ ├── ReadFileException.py │ │ ├── ReadFromPickleException.py │ │ └── __init__.py │ ├── local_launchers │ │ ├── __init__.py │ │ ├── launcher_utils.py │ │ ├── local_collector_launcher.py │ │ ├── local_exporter_launcher.py │ │ ├── local_method_launcher.py │ │ └── local_query_launcher.py │ ├── plotters │ │ ├── R │ │ │ ├── plot_dot_by_column_name.R │ │ │ └── plot_heatmaps.R │ │ ├── __init__.py │ │ └── r_plotter.py │ └── tests │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── cellphone_flask_test_case.py │ │ ├── fixtures │ │ ├── analysis__deconvoluted_result__data-test_custom_counts_data_threshold-01_precision-1.txt │ │ ├── analysis__deconvoluted_result__data-test_subsampled_threshold-01_precision-3.txt │ │ ├── analysis__deconvoluted_result__data-test_threshold-01_precision-1.txt │ │ ├── analysis__deconvoluted_result__data-test_threshold-01_precision-3.txt │ │ ├── analysis__means_result__data-test_custom_counts_data_threshold-01_precision-1.txt │ │ ├── analysis__means_result__data-test_subsampled_threshold-01_precision-3.txt │ │ ├── analysis__means_result__data-test_threshold-01_precision-1.txt │ │ ├── analysis__means_result__data-test_threshold-01_precision-3.txt │ │ ├── analysis__significant_means_result__data-test_custom_counts_data_threshold-01_precision-1.txt │ │ ├── analysis__significant_means_result__data-test_subsampled_threshold-01_precision-3.txt │ │ ├── analysis__significant_means_result__data-test_threshold-01_precision-1.txt │ │ ├── analysis__significant_means_result__data-test_threshold-01_precision-3.txt │ │ ├── collect_complex.csv │ │ ├── collect_gene.csv │ │ ├── collect_interaction.csv │ │ ├── collect_protein.csv │ │ ├── dot_plot_columns.txt │ │ ├── dot_plot_rows.txt │ │ ├── hi_test_counts.txt │ │ ├── hi_test_custom_counts_data_counts_gene_name.txt │ │ ├── hi_test_custom_counts_data_counts_hgnc_symbol.txt │ │ ├── hi_test_custom_counts_data_meta.txt │ │ ├── hi_test_meta.txt │ │ ├── hi_test_subsampled_counts.txt │ │ ├── hi_test_subsampled_meta.txt │ │ ├── input_for_plot_statistical_analysis__means_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── input_for_plot_statistical_analysis__pvalues_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── integrin_enabled_interactions.csv │ │ ├── integrin_interactions.csv │ │ ├── integrin_proteins.csv │ │ ├── query_cells_to_clusters.csv │ │ ├── query_counts.csv │ │ ├── query_meta.csv │ │ ├── real_counts.csv │ │ ├── real_meta.csv │ │ ├── statistical_analysis__deconvoluted_result__data-test_custom_counts_data_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__deconvoluted_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__deconvoluted_result__data-test_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__deconvoluted_result__data-test_subsampled_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__means_result__data-test_custom_counts_data_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__means_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__means_result__data-test_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__means_result__data-test_subsampled_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__pvalues_result__data-test_custom_counts_data_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__pvalues_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__pvalues_result__data-test_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__pvalues_result__data-test_subsampled_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── statistical_analysis__significant_means_result__data-test_custom_counts_data_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__significant_means_result__data-test_it-10_seed-0_threshold-01_precision-1.txt │ │ ├── statistical_analysis__significant_means_result__data-test_it-10_seed-0_threshold-01_precision-3.txt │ │ └── statistical_analysis__significant_means_result__data-test_subsampled_it-10_seed-0_threshold-01_precision-3.txt │ │ ├── methods │ │ ├── __init__.py │ │ ├── test_terminal_method_analysis.py │ │ └── test_terminal_method_statistical_analysis.py │ │ ├── out │ │ └── .gitkeep │ │ ├── plots │ │ ├── __init__.py │ │ └── test_plots.py │ │ ├── queries │ │ ├── __init__.py │ │ ├── test_terminal_query_interaction_calls.py │ │ └── test_web_api_query_interaction_calls.py │ │ ├── test_collection_calls.py │ │ ├── test_database.py │ │ ├── test_exporter_calls.py │ │ └── test_validators │ │ ├── __init__.py │ │ ├── test_database_relations.py │ │ ├── test_validator_database_number_of_entries.py │ │ └── test_validator_database_random_entries.py ├── tools │ ├── .gitignore │ ├── __init__.py │ ├── actions │ │ ├── __init__.py │ │ └── gene_actions.py │ ├── app.py │ ├── generate_data │ │ ├── __init__.py │ │ ├── filters │ │ │ ├── __init__.py │ │ │ ├── non_complex_interactions.py │ │ │ ├── remove_genes.py │ │ │ └── remove_interactions.py │ │ ├── getters │ │ │ ├── __init__.py │ │ │ ├── get_imex.py │ │ │ └── get_iuphar.py │ │ ├── mergers │ │ │ ├── __init__.py │ │ │ ├── add_curated.py │ │ │ ├── merge_interactions.py │ │ │ └── mergers_genes.py │ │ └── parsers │ │ │ ├── __init__.py │ │ │ ├── parse_interactions_imex.py │ │ │ └── parse_iuphar_guidetopharmacology.py │ ├── interactions_helper.py │ ├── tools_helper.py │ └── validators │ │ ├── __init__.py │ │ └── gene_validators.py └── utils │ ├── __init__.py │ ├── dataframe_format.py │ ├── dataframe_functions.py │ ├── tests │ ├── __init__.py │ ├── fixtures │ │ ├── example_data.csv │ │ ├── example_data.tsv │ │ ├── example_data.txt │ │ └── example_data_custom.csv │ ├── test_dataframe_same_data.py │ └── test_open_data_file.py │ ├── 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