├── .dockerignore ├── .github └── workflows │ ├── docker-publish.yml │ ├── publish-docs-on-github.yml │ ├── publish-to-pypi.yml │ └── python-app.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── LICENSE.md ├── README.md ├── docs ├── .nojekyll ├── Makefile ├── make.bat └── source │ ├── _static │ ├── css │ │ └── immuneml.css │ ├── files │ │ ├── airrc_tutorial │ │ │ ├── 100_extra_receptors.tsv │ │ │ ├── 100_receptors.tsv │ │ │ ├── command_line_backbone.yaml │ │ │ ├── galaxy_backbone.yaml │ │ │ ├── ml_application.yaml │ │ │ ├── receptor_classification.yaml │ │ │ └── slides_example.yaml │ │ ├── dataset.zip │ │ ├── immuneSIM_for_ML.R │ │ ├── metadata_full_sim.csv │ │ ├── ml_methods_properties.csv │ │ ├── quickstart │ │ │ ├── cli │ │ │ │ └── quickstart.yaml │ │ │ └── galaxy │ │ │ │ └── quickstart.yaml │ │ ├── quickstart_data.zip │ │ ├── receptors.tsv │ │ ├── regex_file.tsv │ │ ├── relevant_sequences.csv │ │ └── sequences.tsv │ └── images │ │ ├── 3mer_to_3d.png │ │ ├── ML_setting.png │ │ ├── analysis_paths_receptors.png │ │ ├── analysis_paths_repertoires.png │ │ ├── analysis_paths_sequences.png │ │ ├── definitions_instructions_overview.png │ │ ├── dev_docs │ │ ├── data_model_architecture.png │ │ ├── extending_immuneML.png │ │ ├── immuneML_packages.png │ │ ├── run_python_test_in_test.png │ │ └── running_immuneML.png │ │ ├── example_receptors_file.png │ │ ├── execution_model.png │ │ ├── galaxy │ │ ├── create_dataset_from_collection.png │ │ ├── edit_attributes.png │ │ ├── editor.png │ │ ├── galaxy_failed_html.png │ │ ├── galaxy_history_as_tool_input.png │ │ ├── galaxy_mlsettingsperformance.png │ │ ├── galaxy_train_ml_model.png │ │ ├── galaxy_train_ml_model_expanded.png │ │ ├── galaxy_train_ml_model_expanded_buttons.png │ │ ├── galaxy_train_ml_model_results.png │ │ ├── galaxy_train_ml_model_results_gray.png │ │ ├── galaxy_train_ml_model_results_red.png │ │ ├── galaxy_train_ml_model_results_simplified.png │ │ ├── galaxy_train_ml_model_results_yellow.png │ │ ├── galaxy_train_ml_model_simplified.png │ │ ├── galaxy_upload_data.png │ │ ├── import_galaxy_history.png │ │ ├── ireceptor_gateway.png │ │ ├── report_bug.png │ │ └── visualize_this_data.png │ │ ├── hp_optimization.png │ │ ├── hp_optmization_with_outputs.png │ │ ├── labels_organization.png │ │ ├── metadata.png │ │ ├── metadata_repertoire_classification.png │ │ ├── ml_process_overview.png │ │ ├── nested_cv_overview.png │ │ ├── quickstart.png │ │ ├── quickstart_receptor-level.png │ │ ├── receptor_classification_overview.png │ │ ├── receptor_cnn_immuneML.png │ │ ├── repertoire_classification_overview.png │ │ ├── reports │ │ ├── amino_acid_frequency.png │ │ ├── amino_acid_frequency_change.png │ │ ├── coefficients_logistic_regression.png │ │ ├── deeprc_ig_inputs.png │ │ ├── deeprc_ig_kernels.png │ │ ├── feature_comparison_full.png │ │ ├── feature_comparison_zoom.png │ │ ├── feature_distribution.png │ │ ├── feature_value_barplot.png │ │ ├── motif_seed_recovery.png │ │ ├── tcrdist_motif_a.svg │ │ └── tcrdist_motif_b.svg │ │ ├── sequence_length_distribution.png │ │ ├── simulate_immune_receptor_dataset.png │ │ ├── simulate_immune_repertoire_dataset.png │ │ ├── simulation_implanting.png │ │ ├── state_hierarchy_hp_optimization.png │ │ ├── usability_tutorial │ │ ├── V_gene_dist.png │ │ ├── aa_freq_dist.png │ │ ├── bacc_per_batch.png │ │ ├── dim_red_with_label.png │ │ ├── feature_val_comp.png │ │ └── roc_full.png │ │ ├── usecases │ │ ├── benchmarking.png │ │ ├── emerson_reproduction.png │ │ ├── emerson_robustness.png │ │ ├── epitope_1.png │ │ ├── epitope_2.png │ │ ├── epitope_3.png │ │ ├── immcantation_pcproperties_plot.pdf │ │ ├── immcantation_pcproperties_plot.png │ │ ├── immcantation_vgene_count_plot.pdf │ │ ├── immcantation_vgene_count_plot.png │ │ ├── immunarch_geneusage_plot.pdf │ │ ├── immunarch_geneusage_plot.png │ │ ├── immuneSIML.png │ │ ├── immuneSIML_table.png │ │ └── suppl_fig_use_case_3.png │ │ └── yaml_structure.png │ ├── _templates │ └── layout.html │ ├── airrc_tutorial.rst │ ├── conf.py │ ├── developer_docs.rst │ ├── developer_docs │ ├── caching.rst │ ├── class_documentation_standards.rst │ ├── coding_conventions_and_tips.rst │ ├── data_model.rst │ ├── encoded_data_object.rst │ ├── example_code │ │ ├── RandomDataPlot.py │ │ ├── SillyClassifier.py │ │ ├── SillyEncoder.py │ │ ├── SillyFilter.py │ │ ├── _test_randomDataPlot.py │ │ ├── _test_sillyClassifier.py │ │ ├── _test_sillyEncoder.py │ │ └── _test_sillyFilter.py │ ├── execution_flow.rst │ ├── how_to_add_new_ML_method.rst │ ├── how_to_add_new_encoding.rst │ ├── how_to_add_new_preprocessing.rst │ ├── how_to_add_new_report.rst │ ├── info_new_developers.rst │ └── install_for_development.rst │ ├── favicon.ico │ ├── galaxy.rst │ ├── galaxy │ ├── galaxy_immunologist_friendly.rst │ ├── galaxy_import_remote_data.rst │ ├── galaxy_intro.rst │ └── galaxy_tools.rst │ ├── implementation_details │ └── hyperparameter_optimization_details.rst │ ├── index.rst │ ├── installation.rst │ ├── installation │ ├── cloud.rst │ ├── install_with_package_manager.rst │ ├── installation_docker.rst │ └── run_quickstart.rst │ ├── quickstart.rst │ ├── quickstart │ ├── cli_yaml.rst │ ├── galaxy_simple.rst │ ├── galaxy_yaml.rst │ └── simulation_quickstart.rst │ ├── specification.rst │ ├── troubleshooting.rst │ ├── tutorials.rst │ ├── tutorials │ ├── analyze_dataset.rst │ ├── clustering_tutorial.rst │ ├── comparing_baseline_motifs.rst │ ├── discover_motifs_classifiers.rst │ ├── discover_motifs_precision_recall.rst │ ├── getting_publication_ready_figures.rst │ ├── how_to_apply_to_new_data.rst │ ├── how_to_combine_multiple_encodings.rst │ ├── how_to_generate_a_random_repertoire_dataset.rst │ ├── how_to_import_the_data_to_immuneML.rst │ ├── how_to_perform_exploratory_analysis.rst │ ├── how_to_properly_train_and_assess_an_ml_model.rst │ ├── how_to_simulate_co-occuring_signals.rst │ ├── how_to_simulate_paired_chain_data.rst │ ├── how_to_train_and_apply_gen_model.rst │ ├── how_to_train_and_assess_a_receptor_or_repertoire_classifier.rst │ ├── ligo_simulation_tutorials.rst │ ├── ligo_simulation_yaml.rst │ ├── motif_recovery.rst │ ├── recovering_simulated_motifs.rst │ └── simulation_with_custom_signal_functions.rst │ ├── usecases.rst │ ├── usecases │ ├── benchmarking_use_case.rst │ ├── emerson_reproduction.rst │ ├── extendability_use_case.rst │ ├── immcantation_use_case.rst │ ├── immunarch_use_case.rst │ └── immunesim_use_case.rst │ └── yaml_specs │ ├── datasets.rst │ ├── encodings.rst │ ├── how_to_specify_an_analysis_with_yaml.rst │ ├── instructions.rst │ ├── ml_methods.rst │ ├── preprocessings.rst │ ├── reports.rst │ ├── simulation.rst │ └── yaml_parameter_details.rst ├── immuneML ├── IO │ ├── __init__.py │ ├── dataset_export │ │ ├── AIRRExporter.py │ │ ├── DataExporter.py │ │ └── __init__.py │ ├── dataset_import │ │ ├── AIRRImport.py │ │ ├── DataImport.py │ │ ├── DatasetImportParams.py │ │ ├── GenericImport.py │ │ ├── IGoRImport.py │ │ ├── IReceptorImport.py │ │ ├── ImmunoSEQRearrangementImport.py │ │ ├── ImmunoSEQSampleImport.py │ │ ├── MiXCRImport.py │ │ ├── OLGAImport.py │ │ ├── RandomReceptorDatasetImport.py │ │ ├── RandomRepertoireDatasetImport.py │ │ ├── RandomSequenceDatasetImport.py │ │ ├── TenxGenomicsImport.py │ │ ├── VDJdbImport.py │ │ ├── __init__.py │ │ └── conversion │ │ │ └── imgt_adaptive_conversion.csv │ └── ml_method │ │ ├── MLExporter.py │ │ ├── MLImport.py │ │ ├── MLMethodConfiguration.py │ │ ├── UtilIO.py │ │ └── __init__.py ├── __init__.py ├── analysis │ ├── SequenceMatcher.py │ ├── __init__.py │ ├── criteria_matches │ │ ├── BooleanType.py │ │ ├── CriteriaMatcher.py │ │ ├── CriteriaTypeInstantiator.py │ │ ├── OperationType.py │ │ └── __init__.py │ ├── data_manipulation │ │ ├── DataReshaper.py │ │ ├── NormalizationType.py │ │ ├── ReductionMethod.py │ │ └── __init__.py │ └── entropy_calculations │ │ ├── EntropyCalculator.py │ │ └── __init__.py ├── api │ ├── __init__.py │ ├── aggregated_runs │ │ ├── MultiDatasetBenchmarkTool.py │ │ └── __init__.py │ └── galaxy │ │ ├── ApplyGenModelTool.py │ │ ├── DataSimulationTool.py │ │ ├── DatasetGenerationOverviewTool.py │ │ ├── DatasetGenerationTool.py │ │ ├── GalaxyMLApplicationTool.py │ │ ├── GalaxySimulationTool.py │ │ ├── GalaxyTool.py │ │ ├── GalaxyTrainGenModel.py │ │ ├── GalaxyTrainMLModel.py │ │ ├── GalaxyYamlTool.py │ │ ├── RepertoireClassificationTool.py │ │ ├── Util.py │ │ ├── __init__.py │ │ ├── build_apply_gen_model_specs.py │ │ ├── build_clustering_yaml.py │ │ ├── build_dataset_overview_yaml.py │ │ ├── build_dummy_data_simulation_yaml.py │ │ ├── build_ligo_yaml.py │ │ ├── build_ml_application_yaml.py │ │ ├── build_train_gen_model_specs.py │ │ └── build_train_ml_model_yaml.py ├── app │ ├── ImmuneMLApp.py │ ├── LigoApp.py │ └── __init__.py ├── caching │ ├── CacheHandler.py │ ├── CacheObjectType.py │ ├── CacheType.py │ └── __init__.py ├── config │ └── default_params │ │ ├── datasets │ │ ├── airr_params.yaml │ │ ├── generic_params.yaml │ │ ├── i_receptor_params.yaml │ │ ├── igor_params.yaml │ │ ├── immuno_seq_rearrangement_params.yaml │ │ ├── immuno_seq_sample_params.yaml │ │ ├── mixcr_params.yaml │ │ ├── olga_params.yaml │ │ ├── random_receptor_dataset_params.yaml │ │ ├── random_repertoire_dataset_params.yaml │ │ ├── random_sequence_dataset_params.yaml │ │ ├── tenx_genomics_params.yaml │ │ └── vdjdb_params.yaml │ │ ├── encodings │ │ ├── atchley_kmer_params.yaml │ │ ├── comp_airr_distance_params.yaml │ │ ├── comp_airr_sequence_abundance_params.yaml │ │ ├── distance_params.yaml │ │ ├── esmc_params.yaml │ │ ├── gene_frequency_params.yaml │ │ ├── kmer_abundance_params.yaml │ │ ├── kmer_frequency_params.yaml │ │ ├── matched_receptors_params.yaml │ │ ├── matched_regex_params.yaml │ │ ├── matched_sequences_params.yaml │ │ ├── motif_params.yaml │ │ ├── one_hot_params.yaml │ │ ├── prot_t5_params.yaml │ │ ├── sequence_abundance_params.yaml │ │ ├── similar_to_positive_sequence_params.yaml │ │ ├── tcr_bert_params.yaml │ │ ├── tcrdist_params.yaml │ │ └── word2_vec_params.yaml │ │ ├── example_weighting │ │ └── predefined_weighting_params.yaml │ │ ├── instructions │ │ ├── clustering_params.yaml │ │ ├── dataset_export.yaml │ │ ├── exploratory_analysis_params.yaml │ │ ├── export_parser_params.yaml │ │ ├── feasibility_summary_params.yaml │ │ ├── ligo_sim_params.yaml │ │ ├── ml_application_params.yaml │ │ ├── split_config_params.yaml │ │ ├── subsampling_params.yaml │ │ ├── train_gen_model_params.yaml │ │ └── train_ml_model_params.yaml │ │ ├── ml_methods │ │ ├── atchley_kmer_mil_classifier_params.yaml │ │ ├── binary_feature_classifier_params.yaml │ │ ├── deep_rc_params.yaml │ │ ├── keras_sequence_cnn_params.yaml │ │ ├── ml_method_params.yaml │ │ ├── probabilistic_binary_classifier_params.yaml │ │ ├── progen_params.yaml │ │ ├── pwm_params.yaml │ │ ├── receptor_cnn_params.yaml │ │ ├── simple_lstm_params.yaml │ │ ├── simple_vae_params.yaml │ │ ├── sonnia_params.yaml │ │ └── tcrdist_classifier_params.yaml │ │ ├── motif_instantiation_strategy │ │ └── gapped_kmer_params.yaml │ │ ├── preprocessing │ │ ├── duplicate_sequence_filter_params.yaml │ │ └── sequence_length_filter_params.yaml │ │ ├── reports │ │ ├── amino_acid_frequency_distribution_params.yaml │ │ ├── coefficients_params.yaml │ │ ├── comp_airr_clustering_report_params.yaml │ │ ├── component_number_exploration_params.yaml │ │ ├── confusion_matrix_per_label_params.yaml │ │ ├── cv_feature_performance_params.yaml │ │ ├── cytoscape_network_exporter_params.yaml │ │ ├── deep_rc_motif_discovery_params.yaml │ │ ├── design_matrix_exporter_params.yaml │ │ ├── disease_associated_sequence_cv_overlap_params.yaml │ │ ├── feature_comparison_params.yaml │ │ ├── feature_value_barplot_params.yaml │ │ ├── kl_gen_model_report.yaml │ │ ├── ml_settings_performance_params.yaml │ │ ├── motif_generalization_analysis_params.yaml │ │ ├── motif_overlap_params.yaml │ │ ├── motif_seed_recovery_params.yaml │ │ ├── motif_test_set_performance_params.yaml │ │ ├── performance_per_label_params.yaml │ │ ├── receptor_dataset_overview_params.yaml │ │ ├── recovered_significant_features_params.yaml │ │ ├── reference_sequence_overlap_params.yaml │ │ ├── repertoire_clonotype_summary_params.yaml │ │ ├── sequence_count_distribution_params.yaml │ │ ├── sequence_length_distribution_params.yaml │ │ ├── significant_features_params.yaml │ │ ├── tcrdist_motif_discovery_params.yaml │ │ ├── vae_summary_params.yaml │ │ └── vj_gene_distribution_params.yaml │ │ └── simulation │ │ ├── ligo_sim_config_item_params.yaml │ │ └── ligo_sim_config_params.yaml ├── data_model │ ├── AIRRSequenceSet.py │ ├── EncodedData.py │ ├── SequenceParams.py │ ├── SequenceSet.py │ ├── __init__.py │ ├── bnp_util.py │ └── datasets │ │ ├── Dataset.py │ │ ├── ElementDataset.py │ │ ├── RepertoireDataset.py │ │ └── __init__.py ├── dev_util │ ├── __init__.py │ └── util.py ├── dsl │ ├── DefaultParamsLoader.py │ ├── ImmuneMLParser.py │ ├── InstructionParser.py │ ├── ObjectParser.py │ ├── OutputParser.py │ ├── Parser.py │ ├── Util.py │ ├── __init__.py │ ├── definition_parsers │ │ ├── DefinitionParser.py │ │ ├── DefinitionParserOutput.py │ │ ├── EncodingParser.py │ │ ├── ExampleWeightingParser.py │ │ ├── MLParser.py │ │ ├── MotifParser.py │ │ ├── PreprocessingParser.py │ │ ├── ReportParser.py │ │ ├── SignalParser.py │ │ ├── SimulationParser.py │ │ └── __init__.py │ ├── import_parsers │ │ ├── ImportParser.py │ │ └── __init__.py │ ├── instruction_parsers │ │ ├── ApplyGenModelParser.py │ │ ├── ClusteringParser.py │ │ ├── DatasetExportParser.py │ │ ├── ExploratoryAnalysisParser.py │ │ ├── FeasibilitySummaryParser.py │ │ ├── LabelHelper.py │ │ ├── LigoSimParser.py │ │ ├── MLApplicationParser.py │ │ ├── SubsamplingParser.py │ │ ├── TrainGenModelParser.py │ │ ├── TrainMLModelParser.py │ │ └── __init__.py │ ├── semantic_model │ │ ├── MLResult.py │ │ ├── SemanticModel.py │ │ └── __init__.py │ └── symbol_table │ │ ├── SymbolTable.py │ │ ├── SymbolTableEntry.py │ │ ├── SymbolType.py │ │ └── __init__.py ├── encodings │ ├── DatasetEncoder.py │ ├── EncoderParams.py │ ├── __init__.py │ ├── abundance_encoding │ │ ├── AbundanceEncoderHelper.py │ │ ├── CompAIRRBatchIterator.py │ │ ├── CompAIRRSequenceAbundanceEncoder.py │ │ ├── KmerAbundanceEncoder.py │ │ ├── SequenceAbundanceEncoder.py │ │ └── __init__.py │ ├── atchley_kmer_encoding │ │ ├── AtchleyKmerEncoder.py │ │ ├── RelativeAbundanceType.py │ │ ├── Util.py │ │ ├── __init__.py │ │ └── atchley_factors.csv │ ├── baseline_encoding │ │ ├── GeneFrequencyEncoder.py │ │ ├── MetadataEncoder.py │ │ └── __init__.py │ ├── composite_encoding │ │ ├── CompositeEncoder.py │ │ └── __init__.py │ ├── deeprc │ │ ├── DeepRCEncoder.py │ │ └── __init__.py │ ├── distance_encoding │ │ ├── CompAIRRDistanceEncoder.py │ │ ├── DistanceEncoder.py │ │ ├── DistanceMetricType.py │ │ ├── TCRdistEncoder.py │ │ └── __init__.py │ ├── diversity_encoding │ │ ├── EvennessProfileEncoder.py │ │ ├── EvennessProfileRepertoireEncoder.py │ │ ├── ShannonDiversityEncoder.py │ │ └── __init__.py │ ├── kmer_frequency │ │ ├── KmerFreqReceptorEncoder.py │ │ ├── KmerFreqRepertoireEncoder.py │ │ ├── KmerFreqSequenceEncoder.py │ │ ├── KmerFrequencyEncoder.py │ │ ├── __init__.py │ │ └── sequence_encoding │ │ │ ├── GappedKmerSequenceEncoder.py │ │ │ ├── IMGTGappedKmerEncoder.py │ │ │ ├── IMGTKmerSequenceEncoder.py │ │ │ ├── KmerSequenceEncoder.py │ │ │ ├── SequenceEncodingStrategy.py │ │ │ ├── SequenceEncodingType.py │ │ │ ├── VGeneContKmerEncoder.py │ │ │ ├── VGeneIMGTKmerEncoder.py │ │ │ └── __init__.py │ ├── motif_encoding │ │ ├── MotifEncoder.py │ │ ├── PositionalMotifHelper.py │ │ ├── PositionalMotifParams.py │ │ ├── SimilarToPositiveSequenceEncoder.py │ │ └── __init__.py │ ├── onehot │ │ ├── OneHotEncoder.py │ │ ├── OneHotReceptorEncoder.py │ │ ├── OneHotRepertoireEncoder.py │ │ ├── OneHotSequenceEncoder.py │ │ └── __init__.py │ ├── preprocessing │ │ ├── FeatureScaler.py │ │ └── __init__.py │ ├── protein_embedding │ │ ├── ESMCEncoder.py │ │ ├── ProtT5Encoder.py │ │ ├── ProteinEmbeddingEncoder.py │ │ ├── TCRBertEncoder.py │ │ └── __init__.py │ ├── reference_encoding │ │ ├── MatchedReceptorsEncoder.py │ │ ├── MatchedReferenceUtil.py │ │ ├── MatchedRegexEncoder.py │ │ ├── MatchedRegexRepertoireEncoder.py │ │ ├── MatchedSequencesEncoder.py │ │ ├── SequenceMatchingSummaryType.py │ │ └── __init__.py │ └── word2vec │ │ ├── W2VRepertoireEncoder.py │ │ ├── W2VSequenceEncoder.py │ │ ├── Word2VecEncoder.py │ │ ├── __init__.py │ │ └── model_creator │ │ ├── KmerPairModelCreator.py │ │ ├── ModelCreatorStrategy.py │ │ ├── ModelType.py │ │ ├── SequenceModelCreator.py │ │ └── __init__.py ├── environment │ ├── Constants.py │ ├── EnvironmentSettings.py │ ├── Label.py │ ├── LabelConfiguration.py │ ├── LabelType.py │ ├── SequenceType.py │ └── __init__.py ├── example_weighting │ ├── ExampleWeightingParams.py │ ├── ExampleWeightingStrategy.py │ ├── __init__.py │ └── predefined_weighting │ │ ├── PredefinedWeighting.py │ │ └── __init__.py ├── hyperparameter_optimization │ ├── HPSetting.py │ ├── HPSettingResult.py │ ├── __init__.py │ ├── config │ │ ├── LeaveOneOutConfig.py │ │ ├── ManualSplitConfig.py │ │ ├── ReportConfig.py │ │ ├── SplitConfig.py │ │ ├── SplitType.py │ │ └── __init__.py │ ├── core │ │ ├── HPAssessment.py │ │ ├── HPSelection.py │ │ ├── HPUtil.py │ │ └── __init__.py │ ├── states │ │ ├── HPAssessmentState.py │ │ ├── HPItem.py │ │ ├── HPLabelState.py │ │ ├── HPSelectionState.py │ │ ├── TrainMLModelState.py │ │ └── __init__.py │ └── strategy │ │ ├── GridSearch.py │ │ ├── HPOptimizationStrategy.py │ │ └── __init__.py ├── ml_methods │ ├── __init__.py │ ├── classifiers │ │ ├── AtchleyKmerMILClassifier.py │ │ ├── BinaryFeatureClassifier.py │ │ ├── DeepRC.py │ │ ├── GradientBoosting.py │ │ ├── KNN.py │ │ ├── KerasSequenceCNN.py │ │ ├── LogRegressionCustomPenalty.py │ │ ├── LogisticRegression.py │ │ ├── MLMethod.py │ │ ├── PrecomputedKNN.py │ │ ├── ProbabilisticBinaryClassifier.py │ │ ├── RandomForestClassifier.py │ │ ├── ReceptorCNN.py │ │ ├── SVC.py │ │ ├── SVM.py │ │ ├── SklearnMethod.py │ │ ├── TCRdistClassifier.py │ │ └── __init__.py │ ├── clustering │ │ ├── AgglomerativeClustering.py │ │ ├── ClusteringMethod.py │ │ ├── DBSCAN.py │ │ ├── HDBSCAN.py │ │ ├── KMeans.py │ │ └── __init__.py │ ├── dim_reduction │ │ ├── DimRedMethod.py │ │ ├── KernelPCA.py │ │ ├── PCA.py │ │ ├── TSNE.py │ │ ├── UMAP.py │ │ └── __init__.py │ ├── generative_models │ │ ├── BackgroundSequences.py │ │ ├── ExperimentalImport.py │ │ ├── GenerativeModel.py │ │ ├── InternalOlgaModel.py │ │ ├── KLEvaluator.py │ │ ├── MultinomialKmerModel.py │ │ ├── OLGA.py │ │ ├── PWM.py │ │ ├── ProGen.py │ │ ├── SequenceTransitionDistribution.py │ │ ├── SimpleLSTM.py │ │ ├── SimpleVAE.py │ │ ├── SoNNia.py │ │ ├── __init__.py │ │ └── progen │ │ │ ├── ProGenConfig.py │ │ │ ├── ProGenForCausalLM.py │ │ │ ├── ProGen_LICENSE.txt │ │ │ └── __init__.py │ ├── helper_methods │ │ ├── FurthestNeighborClassifier.py │ │ └── __init__.py │ ├── pytorch_implementations │ │ ├── PyTorchLogisticRegression.py │ │ ├── PyTorchReceptorCNN.py │ │ ├── SimpleLSTMGenerator.py │ │ ├── SimpleVAEGenerator.py │ │ └── __init__.py │ └── util │ │ ├── Util.py │ │ ├── __init__.py │ │ └── pytorch_util.py ├── ml_metrics │ ├── ClassificationMetric.py │ ├── ClusteringMetric.py │ ├── MetricUtil.py │ ├── __init__.py │ └── ml_metrics.py ├── pairwise_repertoire_comparison │ ├── ComparisonData.py │ ├── ComparisonDataBatch.py │ ├── PairwiseRepertoireComparison.py │ └── __init__.py ├── preprocessing │ ├── Preprocessor.py │ ├── ReferenceSequenceAnnotator.py │ ├── SubjectRepertoireCollector.py │ ├── __init__.py │ └── filters │ │ ├── ChainRepertoireFilter.py │ │ ├── ClonesPerRepertoireFilter.py │ │ ├── CountAggregationFunction.py │ │ ├── CountPerSequenceFilter.py │ │ ├── DuplicateSequenceFilter.py │ │ ├── Filter.py │ │ ├── MetadataFilter.py │ │ ├── SequenceLengthFilter.py │ │ └── __init__.py ├── presentation │ ├── InstructionPresentation.py │ ├── PresentationFactory.py │ ├── PresentationFormat.py │ ├── TemplateParser.py │ ├── __init__.py │ └── html │ │ ├── ClusteringHTMLBuilder.py │ │ ├── DatasetExportHTMLBuilder.py │ │ ├── ExploratoryAnalysisHTMLBuilder.py │ │ ├── FailedGalaxyHTMLBuilder.py │ │ ├── FeasibilitySummaryHTMLBuilder.py │ │ ├── GenModelHTMLBuilder.py │ │ ├── HPHTMLBuilder.py │ │ ├── HTMLBuilder.py │ │ ├── LIgOSimulationHTMLBuilder.py │ │ ├── MLApplicationHTMLBuilder.py │ │ ├── MultiDatasetBenchmarkHTMLBuilder.py │ │ ├── SubsamplingHTMLBuilder.py │ │ ├── Util.py │ │ ├── __init__.py │ │ └── templates │ │ ├── AssessmentSplitDetails.html │ │ ├── Clustering.html │ │ ├── ClusteringSettingDetails.html │ │ ├── ClusteringSplit.html │ │ ├── DatasetExport.html │ │ ├── ExploratoryAnalysis.html │ │ ├── FailedGalaxy.html │ │ ├── FeasibilitySummary.html │ │ ├── GenModel.html │ │ ├── HPOptimization.html │ │ ├── MLApplication.html │ │ ├── MLTraining.html │ │ ├── MultiDatasetBenchmark.html │ │ ├── Reports.html │ │ ├── SelectionDetails.html │ │ ├── Simulation.html │ │ ├── Subsampling.html │ │ ├── css │ │ └── custom.css │ │ └── index.html ├── reports │ ├── PlotlyUtil.py │ ├── Report.py │ ├── ReportOutput.py │ ├── ReportResult.py │ ├── ReportUtil.py │ ├── __init__.py │ ├── clustering_method_reports │ │ ├── ClusteringMethodReport.py │ │ ├── ClusteringVisualization.py │ │ ├── Dendrogram.py │ │ ├── ExternalLabelClusterSummary.py │ │ └── __init__.py │ ├── clustering_reports │ │ ├── ClusteringReport.py │ │ ├── ClusteringStabilityReport.py │ │ ├── ExternalLabelMetricHeatmap.py │ │ └── __init__.py │ ├── data_reports │ │ ├── AminoAcidFrequencyDistribution.py │ │ ├── CompAIRRClusteringReport.py │ │ ├── DataReport.py │ │ ├── GLIPH2Exporter.py │ │ ├── LabelDist.py │ │ ├── LabelOverlap.py │ │ ├── MotifGeneralizationAnalysis.py │ │ ├── NodeDegreeDistribution.py │ │ ├── RecoveredSignificantFeatures.py │ │ ├── RepertoireClonotypeSummary.py │ │ ├── SequenceCountDistribution.py │ │ ├── SequenceLengthDistribution.py │ │ ├── SequencesWithSignificantKmers.py │ │ ├── ShannonDiversityOverview.py │ │ ├── SignificantFeatures.py │ │ ├── SignificantKmerPositions.py │ │ ├── TrueMotifsSummaryBarplot.py │ │ ├── VJGeneDistribution.py │ │ └── __init__.py │ ├── encoding_reports │ │ ├── DesignMatrixExporter.py │ │ ├── DimensionalityReduction.py │ │ ├── EncodingReport.py │ │ ├── FeatureComparison.py │ │ ├── FeatureDistribution.py │ │ ├── FeatureReport.py │ │ ├── FeatureValueBarplot.py │ │ ├── GroundTruthMotifOverlap.py │ │ ├── Matches.py │ │ ├── MotifTestSetPerformance.py │ │ ├── NonMotifSequenceSimilarity.py │ │ ├── PositionalMotifFrequencies.py │ │ ├── RelevantSequenceExporter.py │ │ └── __init__.py │ ├── gen_model_reports │ │ ├── GenModelReport.py │ │ ├── PWMSummary.py │ │ ├── VAESummary.py │ │ └── __init__.py │ ├── ml_reports │ │ ├── BinaryFeaturePrecisionRecall.py │ │ ├── CoefficientPlottingSetting.py │ │ ├── CoefficientPlottingSettingList.py │ │ ├── Coefficients.py │ │ ├── ConfounderAnalysis.py │ │ ├── ConfusionMatrix.py │ │ ├── DeepRCMotifDiscovery.py │ │ ├── KernelSequenceLogo.py │ │ ├── MLReport.py │ │ ├── MotifSeedRecovery.py │ │ ├── ROCCurve.py │ │ ├── SequenceAssociationLikelihood.py │ │ ├── TCRdistMotifDiscovery.py │ │ ├── TrainingPerformance.py │ │ └── __init__.py │ ├── multi_dataset_reports │ │ ├── DiseaseAssociatedSequenceOverlap.py │ │ ├── MultiDatasetReport.py │ │ ├── PerformanceOverview.py │ │ └── __init__.py │ ├── train_gen_model_reports │ │ ├── KLKmerComparison.py │ │ ├── TrainGenModelReport.py │ │ └── __init__.py │ └── train_ml_model_reports │ │ ├── CVFeaturePerformance.py │ │ ├── DiseaseAssociatedSequenceCVOverlap.py │ │ ├── MLSettingsPerformance.py │ │ ├── PerformancePerLabel.py │ │ ├── ROCCurveSummary.py │ │ ├── ReferenceSequenceOverlap.py │ │ ├── TrainMLModelReport.py │ │ └── __init__.py ├── simulation │ ├── LigoSimState.py │ ├── SimConfig.py │ ├── SimConfigItem.py │ ├── __init__.py │ ├── dataset_generation │ │ ├── RandomDatasetGenerator.py │ │ └── __init__.py │ ├── implants │ │ ├── ImplantAnnotation.py │ │ ├── LigoPWM.py │ │ ├── Motif.py │ │ ├── MotifInstance.py │ │ ├── SeedMotif.py │ │ ├── Signal.py │ │ └── __init__.py │ ├── simulation_strategy │ │ ├── ImplantingStrategy.py │ │ ├── RejectionSamplingStrategy.py │ │ ├── SimulationStrategy.py │ │ └── __init__.py │ └── util │ │ ├── __init__.py │ │ ├── bnp_util.py │ │ ├── igor_helper.py │ │ ├── signal_annotation.py │ │ └── util.py ├── util │ ├── AdaptiveImportHelper.py │ ├── CompAIRRHelper.py │ ├── CompAIRRParams.py │ ├── DistanceMetrics.py │ ├── DocEnumHelper.py │ ├── EncoderHelper.py │ ├── ExporterHelper.py │ ├── FilenameHandler.py │ ├── ImportHelper.py │ ├── KmerHelper.py │ ├── Logger.py │ ├── MotifPerformancePlotHelper.py │ ├── NameBuilder.py │ ├── NumpyHelper.py │ ├── ParameterValidator.py │ ├── PathBuilder.py │ ├── PositionHelper.py │ ├── ReadsType.py │ ├── ReflectionHandler.py │ ├── RepertoireBuilder.py │ ├── SequenceAnalysisHelper.py │ ├── SignificantFeaturesHelper.py │ ├── StringHelper.py │ ├── TCRdistHelper.py │ └── __init__.py └── workflows │ ├── __init__.py │ ├── instructions │ ├── Instruction.py │ ├── MLProcess.py │ ├── TrainMLModelInstruction.py │ ├── __init__.py │ ├── apply_gen_model │ │ ├── ApplyGenModelInstruction.py │ │ └── __init__.py │ ├── clustering │ │ ├── ClusteringInstruction.py │ │ ├── ClusteringReportHandler.py │ │ ├── ClusteringRunner.py │ │ ├── ClusteringState.py │ │ ├── ValidationHandler.py │ │ ├── __init__.py │ │ └── clustering_run_model.py │ ├── dataset_generation │ │ ├── DatasetExportInstruction.py │ │ ├── DatasetExportState.py │ │ └── __init__.py │ ├── exploratory_analysis │ │ ├── ExploratoryAnalysisInstruction.py │ │ ├── ExploratoryAnalysisState.py │ │ ├── ExploratoryAnalysisUnit.py │ │ └── __init__.py │ ├── ligo_sim_feasibility │ │ ├── FeasibilitySummaryInstruction.py │ │ ├── __init__.py │ │ └── feasibility_reports.py │ ├── ligo_simulation │ │ ├── LigoSimInstruction.py │ │ ├── __init__.py │ │ └── runtime_reports.py │ ├── ml_model_application │ │ ├── MLApplicationInstruction.py │ │ ├── MLApplicationState.py │ │ └── __init__.py │ ├── quickstart.py │ ├── subsampling │ │ ├── SubsamplingInstruction.py │ │ ├── SubsamplingState.py │ │ └── __init__.py │ └── train_gen_model │ │ ├── TrainGenModelInstruction.py │ │ └── __init__.py │ └── steps │ ├── DataEncoder.py │ ├── DataEncoderParams.py │ ├── DataWeighter.py │ ├── DataWeighterParams.py │ ├── MLMethodAssessment.py │ ├── MLMethodAssessmentParams.py │ ├── MLMethodTrainer.py │ ├── MLMethodTrainerParams.py │ ├── Step.py │ ├── StepParams.py │ ├── __init__.py │ └── data_splitter │ ├── DataSplitter.py │ ├── DataSplitterParams.py │ ├── LeaveOneOutSplitter.py │ ├── ManualSplitter.py │ ├── Util.py │ └── __init__.py ├── pyproject.toml ├── requirements.txt ├── requirements_DeepRC.txt ├── requirements_KerasSequenceCNN.txt ├── requirements_TCRdist.txt ├── requirements_generative_models.txt ├── requirements_sphinx.txt ├── scripts ├── DocumentatonFormat.py ├── __init__.py ├── check_new_encoder.py ├── check_new_ml_method.py ├── checker_util.py ├── generate_module_API_docs.sh ├── generate_module_API_docs_github.sh ├── specification_util.py └── specs_docs_generation.py ├── test ├── IO │ ├── __init__.py │ ├── dataset_export │ │ ├── __init__.py │ │ └── test_AIRRExporter.py │ └── dataset_import │ │ ├── __init__.py │ │ ├── test_AIRRImport.py │ │ ├── test_IGoRImport.py │ │ ├── test_ImmunoSEQRearrangementImport.py │ │ ├── test_OLGAImport.py │ │ ├── test_VDJdbImport.py │ │ ├── test_genericImport.py │ │ ├── test_iReceptorImport.py │ │ ├── test_immunoSEQSampleImport.py │ │ ├── test_miXCRImport.py │ │ └── test_tenxGenomicsImport.py ├── __init__.py ├── analysis │ ├── __init__.py │ ├── criteria_matches │ │ ├── __init__.py │ │ ├── test_criteriaMatcher.py │ │ └── test_criteriaTypeInstantiator.py │ ├── entropy_calculations │ │ ├── __init__.py │ │ └── test_entropyCalculator.py │ ├── similarities │ │ └── test_repertoireSimilarityComputer.py │ └── test_sequenceMatcher.py ├── api │ ├── __init__.py │ ├── aggregated_runs │ │ ├── __init__.py │ │ └── test_MultiDatasetBenchmarkTool.py │ └── galaxy │ │ ├── __init__.py │ │ ├── test_DataSimulationTool.py │ │ ├── test_DatasetGenerationOverviewTool.py │ │ ├── test_DatasetGenerationTool.py │ │ ├── test_GalaxySimulationTool.py │ │ ├── test_GalaxyTrainGenModel.py │ │ ├── test_GalaxyTrainMLModel.py │ │ ├── test_GalaxyYamlTool.py │ │ ├── test_build_clustering_yaml.py │ │ ├── test_build_dataset_overview_yaml.py │ │ ├── test_build_dummy_data_simulation_yaml.py │ │ ├── test_build_ligo_yaml.py │ │ ├── test_build_ml_application_yaml.py │ │ ├── test_build_train_gen_model_specs.py │ │ ├── test_build_train_ml_model_yaml.py │ │ └── test_repertoireClassificationTool.py ├── app │ ├── __init__.py │ └── test_immuneMLApp.py ├── caching │ ├── __init__.py │ └── test_cacheHandler.py ├── data_model │ ├── __init__.py │ ├── datasets │ │ ├── __init__.py │ │ ├── test_ReceptorDataset.py │ │ ├── test_RepertoireDataset.py │ │ └── test_SequenceDataset.py │ └── repertoire │ │ ├── __init__.py │ │ └── test_repertoire.py ├── dsl │ ├── __init__.py │ ├── instruction_parsers │ │ ├── __init__.py │ │ ├── test_ApplyGenModelParser.py │ │ ├── test_DatasetExportParser.py │ │ ├── test_SubsamplingParser.py │ │ └── test_exploratoryAnalysisParser.py │ ├── test_MLParser.py │ ├── test_defaultParamsLoader.py │ ├── test_exampleWeightingParser.py │ ├── test_immuneMLParser.py │ ├── test_importParser.py │ ├── test_preprocessingParser.py │ ├── test_reportParser.py │ └── test_symbolTable.py ├── encodings │ ├── __init__.py │ ├── atchley_kmer_encoding │ │ ├── __init__.py │ │ └── test_AtchleyKmerEncoder.py │ ├── baseline_encoding │ │ ├── __init__.py │ │ ├── test_gene_frequency_encoder.py │ │ └── test_metadata_encoder.py │ ├── composite_encoding │ │ ├── __init__.py │ │ └── test_composite_encoding.py │ ├── deeprc │ │ ├── __init__.py │ │ └── test_deepRCEncoder.py │ ├── distance_encoding │ │ ├── __init__.py │ │ ├── test_TCRdistEncoder.py │ │ ├── test_compAIRRDistanceEncoder.py │ │ └── test_distanceEncoder.py │ ├── diversity_encoding │ │ ├── __init__.py │ │ ├── test_ShannonDiversityEncoder.py │ │ └── test_evennessProfileEncoder.py │ ├── filtered_sequence_encoding │ │ ├── __init__.py │ │ ├── test_AbundanceEncoderHelper.py │ │ ├── test_CompAIRRSequenceAbundanceEncoder.py │ │ ├── test_KmerAbundanceEncoder.py │ │ └── test_SequenceAbundanceEncoder.py │ ├── kmer_frequency │ │ ├── __init__.py │ │ ├── sequence_encoding │ │ │ ├── __init__.py │ │ │ ├── test_IMGTGappedKmerEncoder.py │ │ │ ├── test_IMGTKmerSequenceEncoder.py │ │ │ ├── test_VGeneIMGTKmerSequenceEncoder.py │ │ │ ├── test_gappedKmerSequenceEncoder.py │ │ │ └── test_kmerSequenceEncoder.py │ │ ├── test_kmerFreqReceptorEncoder.py │ │ ├── test_kmerFreqSequenceEncoder.py │ │ └── test_kmerFrequencyEncoder.py │ ├── motif_encoding │ │ ├── __init__.py │ │ ├── test_MotifEncoder.py │ │ ├── test_PositionalMotifHelper.py │ │ └── test_SimilarToPositiveSequenceEncoder.py │ ├── onehot │ │ ├── __init__.py │ │ ├── test_oneHotEncoder.py │ │ ├── test_oneHotReceptorEncoder.py │ │ └── test_oneHotSequenceEncoder.py │ ├── preprocessing │ │ ├── __init__.py │ │ └── test_featureScaler.py │ ├── protein_embedding_encoders │ │ ├── __init__.py │ │ ├── test_esmc_encoder.py │ │ ├── test_prott5_encoder.py │ │ └── test_tcr_bert_encoder.py │ ├── reference_encoding │ │ ├── __init__.py │ │ ├── test_matchedReceptorsEncoder.py │ │ ├── test_matchedRegexEncoder.py │ │ └── test_matchedSequencesEncoder.py │ ├── test_esmc_encoder.py │ └── word2vec │ │ ├── __init__.py │ │ ├── model_creator │ │ ├── __init__.py │ │ ├── test_kmerPairModelCreator.py │ │ └── test_sequenceModelCreator.py │ │ └── test_word2VecEncoder.py ├── example_weighting │ └── importance_weighting │ │ └── test_predefinedWeighting.py ├── hyperparameter_optimization │ ├── __init__.py │ └── strategy │ │ ├── __init__.py │ │ └── test_gridSearch.py ├── integration_tests │ ├── __init__.py │ ├── test_ML_import_export.py │ ├── test_clustering_workflow.py │ ├── test_composite_encoding_and_custom_penalty.py │ ├── test_custom_signal_func.py │ ├── test_cv_split_variants.py │ ├── test_dataset_export_html_output.py │ ├── test_dendrogram.py │ ├── test_exploratoryAnalysisDesignMatrixExporter.py │ ├── test_exploratory_analysis_with_dim_reduction.py │ ├── test_fesibility_summary.py │ ├── test_fit_apply_gen_model.py │ ├── test_galaxy_workflow.py │ ├── test_importance_sampling.py │ ├── test_ligo_multiple_signal_simulation.py │ ├── test_ligo_simulation.py │ ├── test_paired_simulation.py │ ├── test_random_dataset_workflow.py │ ├── test_receptorClassification.py │ ├── test_receptor_cnn_workflow.py │ ├── test_sequenceAbundanceEncoding.py │ ├── test_sequenceClassification.py │ ├── test_simulation.py │ └── test_subsampling.py ├── ml_methods │ ├── __init__.py │ ├── test_BinaryFeatureClassifier.py │ ├── test_ProbabilisticBinaryClassifier.py │ ├── test_ReceptorCNN.py │ ├── test_SVC.py │ ├── test_SVM.py │ ├── test_TCRdistClassifier.py │ ├── test_atchleyKmerMILClassifier.py │ ├── test_deepRC.py │ ├── test_kNN.py │ ├── test_kerasSequenceCNN.py │ ├── test_logisticRegression.py │ ├── test_progen.py │ ├── test_randomForestClassifier.py │ ├── test_simple_lstm.py │ ├── test_simple_vae.py │ └── test_sklearnMethod.py ├── pairwise_repertoire_comparison │ ├── __init__.py │ ├── test_comparisonData.py │ └── test_pairwiseRepertoireComparison.py ├── preprocessing │ ├── __init__.py │ ├── filters │ │ ├── __init__.py │ │ ├── test_SequenceLengthFilter.py │ │ ├── test_chainRepertoireFilter.py │ │ ├── test_clonesPerRepertoireFilter.py │ │ ├── test_countPerSequenceFilter.py │ │ ├── test_duplicateSequenceFilter.py │ │ └── test_metadataFilter.py │ ├── test_ReferenceSequenceAnnotator.py │ └── test_subjectRepertoireCollector.py ├── presentation │ ├── __init__.py │ └── html │ │ ├── __init__.py │ │ └── test_ExploratoryAnalysisHTMLBuilder.py ├── reports │ ├── __init__.py │ ├── analysis_reports │ │ ├── __init__.py │ │ └── test_CVFeaturePerformance.py │ ├── data_reports │ │ ├── __init__.py │ │ ├── test_AminoAcidFrequencyDistribution.py │ │ ├── test_GLIPH2Exporter.py │ │ ├── test_MotifGeneralizationAnalysis.py │ │ ├── test_NodeDegreeDistribution.py │ │ ├── test_RecoveredSignificantFeatures.py │ │ ├── test_RepertoireClonotypeSummary.py │ │ ├── test_SequencesWithSignificantKmers.py │ │ ├── test_SignificantFeatures.py │ │ ├── test_SignificantKmerPositions.py │ │ ├── test_VJGeneDistribution.py │ │ ├── test_compairr_clustering_report.py │ │ ├── test_label_overlap.py │ │ ├── test_sequenceCountDistribution.py │ │ ├── test_sequenceLengthDistribution.py │ │ ├── test_shannon_diversity_overview.py │ │ └── test_true_motifs_summary_barplot.py │ ├── encoding_reports │ │ ├── __init__.py │ │ ├── test_DesignMatrixExporter.py │ │ ├── test_FeatureDistribution.py │ │ ├── test_GroundTruthMotifOverlap.py │ │ ├── test_Matches.py │ │ ├── test_MotifTestSetPerformance.py │ │ ├── test_NonMotifSequenceSimilarity.py │ │ ├── test_PositionalMotifFrequencies.py │ │ ├── test_RelevantSequenceExporter.py │ │ ├── test_TCRdistMotifDiscovery.py │ │ ├── test_featureComparison.py │ │ └── test_featureValueBarplot.py │ ├── gen_model_reports │ │ ├── __init__.py │ │ ├── test_KLGenModelReport.py │ │ ├── test_pwm_summary.py │ │ └── test_vae_summary.py │ ├── hyperparameter │ │ ├── __init__.py │ │ ├── test_DiseaseAssociatedSequenceCVOverlap.py │ │ └── test_ReferenceSequenceOverlap.py │ ├── ml_reports │ │ ├── __init__.py │ │ ├── test_BinaryFeaturePrecisionRecall.py │ │ ├── test_KernelSequenceLogo.py │ │ ├── test_ROCCurve.py │ │ ├── test_SequenceAssociationLikelihood.py │ │ ├── test_TrainingPerformance.py │ │ ├── test_coefficients.py │ │ ├── test_conf_matrix.py │ │ ├── test_counfounderAnalysis.py │ │ ├── test_mLSettingsPerformance.py │ │ └── test_motifSeedRecovery.py │ └── tool_reports │ │ ├── __init__.py │ │ ├── test_DiseaseAssociatedSequenceOverlap.py │ │ └── test_PerformanceOverview.py ├── simulation │ ├── __init__.py │ ├── dataset_generation │ │ ├── __init__.py │ │ └── test_RandomDatasetGenerator.py │ ├── signal_implanting_strategy │ │ └── sequence_implanting │ │ │ └── test_gappedMotifImplanting.py │ ├── test_implanting.py │ ├── test_signal_annotation.py │ ├── test_util.py │ └── util │ │ ├── __init__.py │ │ └── test_igor_helper.py ├── util │ ├── __init__.py │ ├── test_StringHelper.py │ ├── test_filenameHandler.py │ ├── test_kmerHelper.py │ ├── test_nameBuilder.py │ ├── test_pathBuilder.py │ ├── test_positionHelper.py │ ├── test_reflectionHandler.py │ └── test_repertoireBuilder.py └── workflows │ ├── __init__.py │ ├── instructions │ ├── __init__.py │ ├── test_ApplyGenModelInstruction.py │ ├── test_DatasetExportInstruction.py │ ├── test_MLApplicationInstruction.py │ ├── test_SubsamplingInstruction.py │ ├── test_exploratoryAnalysisInstruction.py │ ├── test_quickstart.py │ └── 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