LICENSE.md
README.md
pyproject.toml
docs/source/conf.py
docs/source/developer_docs/example_code/RandomDataPlot.py
docs/source/developer_docs/example_code/SillyClassifier.py
docs/source/developer_docs/example_code/SillyEncoder.py
docs/source/developer_docs/example_code/SillyFilter.py
docs/source/developer_docs/example_code/_test_randomDataPlot.py
docs/source/developer_docs/example_code/_test_sillyClassifier.py
docs/source/developer_docs/example_code/_test_sillyEncoder.py
docs/source/developer_docs/example_code/_test_sillyFilter.py
immuneML/__init__.py
immuneML.egg-info/PKG-INFO
immuneML.egg-info/SOURCES.txt
immuneML.egg-info/dependency_links.txt
immuneML.egg-info/entry_points.txt
immuneML.egg-info/requires.txt
immuneML.egg-info/top_level.txt
immuneML/IO/__init__.py
immuneML/IO/dataset_export/AIRRExporter.py
immuneML/IO/dataset_export/DataExporter.py
immuneML/IO/dataset_export/__init__.py
immuneML/IO/dataset_import/AIRRImport.py
immuneML/IO/dataset_import/DataImport.py
immuneML/IO/dataset_import/DatasetImportParams.py
immuneML/IO/dataset_import/GenericImport.py
immuneML/IO/dataset_import/IGoRImport.py
immuneML/IO/dataset_import/IReceptorImport.py
immuneML/IO/dataset_import/ImmunoSEQRearrangementImport.py
immuneML/IO/dataset_import/ImmunoSEQSampleImport.py
immuneML/IO/dataset_import/MiXCRImport.py
immuneML/IO/dataset_import/OLGAImport.py
immuneML/IO/dataset_import/RandomReceptorDatasetImport.py
immuneML/IO/dataset_import/RandomRepertoireDatasetImport.py
immuneML/IO/dataset_import/RandomSequenceDatasetImport.py
immuneML/IO/dataset_import/TenxGenomicsImport.py
immuneML/IO/dataset_import/VDJdbImport.py
immuneML/IO/dataset_import/__init__.py
immuneML/IO/dataset_import/conversion/imgt_adaptive_conversion.csv
immuneML/IO/ml_method/MLExporter.py
immuneML/IO/ml_method/MLImport.py
immuneML/IO/ml_method/MLMethodConfiguration.py
immuneML/IO/ml_method/UtilIO.py
immuneML/IO/ml_method/__init__.py
immuneML/analysis/SequenceMatcher.py
immuneML/analysis/__init__.py
immuneML/analysis/criteria_matches/BooleanType.py
immuneML/analysis/criteria_matches/CriteriaMatcher.py
immuneML/analysis/criteria_matches/CriteriaTypeInstantiator.py
immuneML/analysis/criteria_matches/OperationType.py
immuneML/analysis/criteria_matches/__init__.py
immuneML/analysis/data_manipulation/DataReshaper.py
immuneML/analysis/data_manipulation/NormalizationType.py
immuneML/analysis/data_manipulation/ReductionMethod.py
immuneML/analysis/data_manipulation/__init__.py
immuneML/analysis/entropy_calculations/EntropyCalculator.py
immuneML/analysis/entropy_calculations/__init__.py
immuneML/api/__init__.py
immuneML/api/aggregated_runs/MultiDatasetBenchmarkTool.py
immuneML/api/aggregated_runs/__init__.py
immuneML/api/galaxy/ApplyGenModelTool.py
immuneML/api/galaxy/DataSimulationTool.py
immuneML/api/galaxy/DatasetGenerationOverviewTool.py
immuneML/api/galaxy/DatasetGenerationTool.py
immuneML/api/galaxy/GalaxyMLApplicationTool.py
immuneML/api/galaxy/GalaxySimulationTool.py
immuneML/api/galaxy/GalaxyTool.py
immuneML/api/galaxy/GalaxyTrainGenModel.py
immuneML/api/galaxy/GalaxyTrainMLModel.py
immuneML/api/galaxy/GalaxyYamlTool.py
immuneML/api/galaxy/RepertoireClassificationTool.py
immuneML/api/galaxy/Util.py
immuneML/api/galaxy/__init__.py
immuneML/api/galaxy/build_apply_gen_model_specs.py
immuneML/api/galaxy/build_clustering_yaml.py
immuneML/api/galaxy/build_dataset_overview_yaml.py
immuneML/api/galaxy/build_dummy_data_simulation_yaml.py
immuneML/api/galaxy/build_ligo_yaml.py
immuneML/api/galaxy/build_ml_application_yaml.py
immuneML/api/galaxy/build_train_gen_model_specs.py
immuneML/api/galaxy/build_train_ml_model_yaml.py
immuneML/app/ImmuneMLApp.py
immuneML/app/LigoApp.py
immuneML/app/__init__.py
immuneML/caching/CacheHandler.py
immuneML/caching/CacheObjectType.py
immuneML/caching/CacheType.py
immuneML/caching/__init__.py
immuneML/config/default_params/datasets/airr_params.yaml
immuneML/config/default_params/datasets/generic_params.yaml
immuneML/config/default_params/datasets/i_receptor_params.yaml
immuneML/config/default_params/datasets/igor_params.yaml
immuneML/config/default_params/datasets/immuno_seq_rearrangement_params.yaml
immuneML/config/default_params/datasets/immuno_seq_sample_params.yaml
immuneML/config/default_params/datasets/mixcr_params.yaml
immuneML/config/default_params/datasets/olga_params.yaml
immuneML/config/default_params/datasets/random_receptor_dataset_params.yaml
immuneML/config/default_params/datasets/random_repertoire_dataset_params.yaml
immuneML/config/default_params/datasets/random_sequence_dataset_params.yaml
immuneML/config/default_params/datasets/tenx_genomics_params.yaml
immuneML/config/default_params/datasets/vdjdb_params.yaml
immuneML/config/default_params/encodings/atchley_kmer_params.yaml
immuneML/config/default_params/encodings/comp_airr_distance_params.yaml
immuneML/config/default_params/encodings/comp_airr_sequence_abundance_params.yaml
immuneML/config/default_params/encodings/distance_params.yaml
immuneML/config/default_params/encodings/esmc_params.yaml
immuneML/config/default_params/encodings/gene_frequency_params.yaml
immuneML/config/default_params/encodings/kmer_abundance_params.yaml
immuneML/config/default_params/encodings/kmer_frequency_params.yaml
immuneML/config/default_params/encodings/matched_receptors_params.yaml
immuneML/config/default_params/encodings/matched_regex_params.yaml
immuneML/config/default_params/encodings/matched_sequences_params.yaml
immuneML/config/default_params/encodings/motif_params.yaml
immuneML/config/default_params/encodings/one_hot_params.yaml
immuneML/config/default_params/encodings/prot_t5_params.yaml
immuneML/config/default_params/encodings/sequence_abundance_params.yaml
immuneML/config/default_params/encodings/similar_to_positive_sequence_params.yaml
immuneML/config/default_params/encodings/tcr_bert_params.yaml
immuneML/config/default_params/encodings/tcrdist_params.yaml
immuneML/config/default_params/encodings/word2_vec_params.yaml
immuneML/config/default_params/example_weighting/predefined_weighting_params.yaml
immuneML/config/default_params/instructions/clustering_params.yaml
immuneML/config/default_params/instructions/dataset_export.yaml
immuneML/config/default_params/instructions/exploratory_analysis_params.yaml
immuneML/config/default_params/instructions/export_parser_params.yaml
immuneML/config/default_params/instructions/feasibility_summary_params.yaml
immuneML/config/default_params/instructions/ligo_sim_params.yaml
immuneML/config/default_params/instructions/ml_application_params.yaml
immuneML/config/default_params/instructions/split_config_params.yaml
immuneML/config/default_params/instructions/subsampling_params.yaml
immuneML/config/default_params/instructions/train_gen_model_params.yaml
immuneML/config/default_params/instructions/train_ml_model_params.yaml
immuneML/config/default_params/ml_methods/atchley_kmer_mil_classifier_params.yaml
immuneML/config/default_params/ml_methods/binary_feature_classifier_params.yaml
immuneML/config/default_params/ml_methods/deep_rc_params.yaml
immuneML/config/default_params/ml_methods/keras_sequence_cnn_params.yaml
immuneML/config/default_params/ml_methods/ml_method_params.yaml
immuneML/config/default_params/ml_methods/probabilistic_binary_classifier_params.yaml
immuneML/config/default_params/ml_methods/progen_params.yaml
immuneML/config/default_params/ml_methods/pwm_params.yaml
immuneML/config/default_params/ml_methods/receptor_cnn_params.yaml
immuneML/config/default_params/ml_methods/simple_lstm_params.yaml
immuneML/config/default_params/ml_methods/simple_vae_params.yaml
immuneML/config/default_params/ml_methods/sonnia_params.yaml
immuneML/config/default_params/ml_methods/tcrdist_classifier_params.yaml
immuneML/config/default_params/motif_instantiation_strategy/gapped_kmer_params.yaml
immuneML/config/default_params/preprocessing/duplicate_sequence_filter_params.yaml
immuneML/config/default_params/preprocessing/sequence_length_filter_params.yaml
immuneML/config/default_params/reports/amino_acid_frequency_distribution_params.yaml
immuneML/config/default_params/reports/coefficients_params.yaml
immuneML/config/default_params/reports/comp_airr_clustering_report_params.yaml
immuneML/config/default_params/reports/component_number_exploration_params.yaml
immuneML/config/default_params/reports/confusion_matrix_per_label_params.yaml
immuneML/config/default_params/reports/cv_feature_performance_params.yaml
immuneML/config/default_params/reports/cytoscape_network_exporter_params.yaml
immuneML/config/default_params/reports/deep_rc_motif_discovery_params.yaml
immuneML/config/default_params/reports/design_matrix_exporter_params.yaml
immuneML/config/default_params/reports/disease_associated_sequence_cv_overlap_params.yaml
immuneML/config/default_params/reports/feature_comparison_params.yaml
immuneML/config/default_params/reports/feature_value_barplot_params.yaml
immuneML/config/default_params/reports/kl_gen_model_report.yaml
immuneML/config/default_params/reports/ml_settings_performance_params.yaml
immuneML/config/default_params/reports/motif_generalization_analysis_params.yaml
immuneML/config/default_params/reports/motif_overlap_params.yaml
immuneML/config/default_params/reports/motif_seed_recovery_params.yaml
immuneML/config/default_params/reports/motif_test_set_performance_params.yaml
immuneML/config/default_params/reports/performance_per_label_params.yaml
immuneML/config/default_params/reports/receptor_dataset_overview_params.yaml
immuneML/config/default_params/reports/recovered_significant_features_params.yaml
immuneML/config/default_params/reports/reference_sequence_overlap_params.yaml
immuneML/config/default_params/reports/repertoire_clonotype_summary_params.yaml
immuneML/config/default_params/reports/sequence_count_distribution_params.yaml
immuneML/config/default_params/reports/sequence_length_distribution_params.yaml
immuneML/config/default_params/reports/significant_features_params.yaml
immuneML/config/default_params/reports/tcrdist_motif_discovery_params.yaml
immuneML/config/default_params/reports/vae_summary_params.yaml
immuneML/config/default_params/reports/vj_gene_distribution_params.yaml
immuneML/config/default_params/simulation/ligo_sim_config_item_params.yaml
immuneML/config/default_params/simulation/ligo_sim_config_params.yaml
immuneML/data_model/AIRRSequenceSet.py
immuneML/data_model/EncodedData.py
immuneML/data_model/SequenceParams.py
immuneML/data_model/SequenceSet.py
immuneML/data_model/__init__.py
immuneML/data_model/bnp_util.py
immuneML/data_model/datasets/Dataset.py
immuneML/data_model/datasets/ElementDataset.py
immuneML/data_model/datasets/RepertoireDataset.py
immuneML/data_model/datasets/__init__.py
immuneML/dev_util/__init__.py
immuneML/dev_util/util.py
immuneML/dsl/DefaultParamsLoader.py
immuneML/dsl/ImmuneMLParser.py
immuneML/dsl/InstructionParser.py
immuneML/dsl/ObjectParser.py
immuneML/dsl/OutputParser.py
immuneML/dsl/Parser.py
immuneML/dsl/Util.py
immuneML/dsl/__init__.py
immuneML/dsl/definition_parsers/DefinitionParser.py
immuneML/dsl/definition_parsers/DefinitionParserOutput.py
immuneML/dsl/definition_parsers/EncodingParser.py
immuneML/dsl/definition_parsers/ExampleWeightingParser.py
immuneML/dsl/definition_parsers/MLParser.py
immuneML/dsl/definition_parsers/MotifParser.py
immuneML/dsl/definition_parsers/PreprocessingParser.py
immuneML/dsl/definition_parsers/ReportParser.py
immuneML/dsl/definition_parsers/SignalParser.py
immuneML/dsl/definition_parsers/SimulationParser.py
immuneML/dsl/definition_parsers/__init__.py
immuneML/dsl/import_parsers/ImportParser.py
immuneML/dsl/import_parsers/__init__.py
immuneML/dsl/instruction_parsers/ApplyGenModelParser.py
immuneML/dsl/instruction_parsers/ClusteringParser.py
immuneML/dsl/instruction_parsers/DatasetExportParser.py
immuneML/dsl/instruction_parsers/ExploratoryAnalysisParser.py
immuneML/dsl/instruction_parsers/FeasibilitySummaryParser.py
immuneML/dsl/instruction_parsers/LabelHelper.py
immuneML/dsl/instruction_parsers/LigoSimParser.py
immuneML/dsl/instruction_parsers/MLApplicationParser.py
immuneML/dsl/instruction_parsers/SubsamplingParser.py
immuneML/dsl/instruction_parsers/TrainGenModelParser.py
immuneML/dsl/instruction_parsers/TrainMLModelParser.py
immuneML/dsl/instruction_parsers/__init__.py
immuneML/dsl/semantic_model/MLResult.py
immuneML/dsl/semantic_model/SemanticModel.py
immuneML/dsl/semantic_model/__init__.py
immuneML/dsl/symbol_table/SymbolTable.py
immuneML/dsl/symbol_table/SymbolTableEntry.py
immuneML/dsl/symbol_table/SymbolType.py
immuneML/dsl/symbol_table/__init__.py
immuneML/encodings/DatasetEncoder.py
immuneML/encodings/EncoderParams.py
immuneML/encodings/__init__.py
immuneML/encodings/abundance_encoding/AbundanceEncoderHelper.py
immuneML/encodings/abundance_encoding/CompAIRRBatchIterator.py
immuneML/encodings/abundance_encoding/CompAIRRSequenceAbundanceEncoder.py
immuneML/encodings/abundance_encoding/KmerAbundanceEncoder.py
immuneML/encodings/abundance_encoding/SequenceAbundanceEncoder.py
immuneML/encodings/abundance_encoding/__init__.py
immuneML/encodings/atchley_kmer_encoding/AtchleyKmerEncoder.py
immuneML/encodings/atchley_kmer_encoding/RelativeAbundanceType.py
immuneML/encodings/atchley_kmer_encoding/Util.py
immuneML/encodings/atchley_kmer_encoding/__init__.py
immuneML/encodings/atchley_kmer_encoding/atchley_factors.csv
immuneML/encodings/baseline_encoding/GeneFrequencyEncoder.py
immuneML/encodings/baseline_encoding/MetadataEncoder.py
immuneML/encodings/baseline_encoding/__init__.py
immuneML/encodings/composite_encoding/CompositeEncoder.py
immuneML/encodings/composite_encoding/__init__.py
immuneML/encodings/deeprc/DeepRCEncoder.py
immuneML/encodings/deeprc/__init__.py
immuneML/encodings/distance_encoding/CompAIRRDistanceEncoder.py
immuneML/encodings/distance_encoding/DistanceEncoder.py
immuneML/encodings/distance_encoding/DistanceMetricType.py
immuneML/encodings/distance_encoding/TCRdistEncoder.py
immuneML/encodings/distance_encoding/__init__.py
immuneML/encodings/diversity_encoding/EvennessProfileEncoder.py
immuneML/encodings/diversity_encoding/EvennessProfileRepertoireEncoder.py
immuneML/encodings/diversity_encoding/ShannonDiversityEncoder.py
immuneML/encodings/diversity_encoding/__init__.py
immuneML/encodings/kmer_frequency/KmerFreqReceptorEncoder.py
immuneML/encodings/kmer_frequency/KmerFreqRepertoireEncoder.py
immuneML/encodings/kmer_frequency/KmerFreqSequenceEncoder.py
immuneML/encodings/kmer_frequency/KmerFrequencyEncoder.py
immuneML/encodings/kmer_frequency/__init__.py
immuneML/encodings/kmer_frequency/sequence_encoding/GappedKmerSequenceEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/IMGTGappedKmerEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/IMGTKmerSequenceEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/KmerSequenceEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/SequenceEncodingStrategy.py
immuneML/encodings/kmer_frequency/sequence_encoding/SequenceEncodingType.py
immuneML/encodings/kmer_frequency/sequence_encoding/VGeneContKmerEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/VGeneIMGTKmerEncoder.py
immuneML/encodings/kmer_frequency/sequence_encoding/__init__.py
immuneML/encodings/motif_encoding/MotifEncoder.py
immuneML/encodings/motif_encoding/PositionalMotifHelper.py
immuneML/encodings/motif_encoding/PositionalMotifParams.py
immuneML/encodings/motif_encoding/SimilarToPositiveSequenceEncoder.py
immuneML/encodings/motif_encoding/__init__.py
immuneML/encodings/onehot/OneHotEncoder.py
immuneML/encodings/onehot/OneHotReceptorEncoder.py
immuneML/encodings/onehot/OneHotRepertoireEncoder.py
immuneML/encodings/onehot/OneHotSequenceEncoder.py
immuneML/encodings/onehot/__init__.py
immuneML/encodings/preprocessing/FeatureScaler.py
immuneML/encodings/preprocessing/__init__.py
immuneML/encodings/protein_embedding/ESMCEncoder.py
immuneML/encodings/protein_embedding/ProtT5Encoder.py
immuneML/encodings/protein_embedding/ProteinEmbeddingEncoder.py
immuneML/encodings/protein_embedding/TCRBertEncoder.py
immuneML/encodings/protein_embedding/__init__.py
immuneML/encodings/reference_encoding/MatchedReceptorsEncoder.py
immuneML/encodings/reference_encoding/MatchedReferenceUtil.py
immuneML/encodings/reference_encoding/MatchedRegexEncoder.py
immuneML/encodings/reference_encoding/MatchedRegexRepertoireEncoder.py
immuneML/encodings/reference_encoding/MatchedSequencesEncoder.py
immuneML/encodings/reference_encoding/SequenceMatchingSummaryType.py
immuneML/encodings/reference_encoding/__init__.py
immuneML/encodings/word2vec/W2VRepertoireEncoder.py
immuneML/encodings/word2vec/W2VSequenceEncoder.py
immuneML/encodings/word2vec/Word2VecEncoder.py
immuneML/encodings/word2vec/__init__.py
immuneML/encodings/word2vec/model_creator/KmerPairModelCreator.py
immuneML/encodings/word2vec/model_creator/ModelCreatorStrategy.py
immuneML/encodings/word2vec/model_creator/ModelType.py
immuneML/encodings/word2vec/model_creator/SequenceModelCreator.py
immuneML/encodings/word2vec/model_creator/__init__.py
immuneML/environment/Constants.py
immuneML/environment/EnvironmentSettings.py
immuneML/environment/Label.py
immuneML/environment/LabelConfiguration.py
immuneML/environment/LabelType.py
immuneML/environment/SequenceType.py
immuneML/environment/__init__.py
immuneML/example_weighting/ExampleWeightingParams.py
immuneML/example_weighting/ExampleWeightingStrategy.py
immuneML/example_weighting/__init__.py
immuneML/example_weighting/predefined_weighting/PredefinedWeighting.py
immuneML/example_weighting/predefined_weighting/__init__.py
immuneML/hyperparameter_optimization/HPSetting.py
immuneML/hyperparameter_optimization/HPSettingResult.py
immuneML/hyperparameter_optimization/__init__.py
immuneML/hyperparameter_optimization/config/LeaveOneOutConfig.py
immuneML/hyperparameter_optimization/config/ManualSplitConfig.py
immuneML/hyperparameter_optimization/config/ReportConfig.py
immuneML/hyperparameter_optimization/config/SplitConfig.py
immuneML/hyperparameter_optimization/config/SplitType.py
immuneML/hyperparameter_optimization/config/__init__.py
immuneML/hyperparameter_optimization/core/HPAssessment.py
immuneML/hyperparameter_optimization/core/HPSelection.py
immuneML/hyperparameter_optimization/core/HPUtil.py
immuneML/hyperparameter_optimization/core/__init__.py
immuneML/hyperparameter_optimization/states/HPAssessmentState.py
immuneML/hyperparameter_optimization/states/HPItem.py
immuneML/hyperparameter_optimization/states/HPLabelState.py
immuneML/hyperparameter_optimization/states/HPSelectionState.py
immuneML/hyperparameter_optimization/states/TrainMLModelState.py
immuneML/hyperparameter_optimization/states/__init__.py
immuneML/hyperparameter_optimization/strategy/GridSearch.py
immuneML/hyperparameter_optimization/strategy/HPOptimizationStrategy.py
immuneML/hyperparameter_optimization/strategy/__init__.py
immuneML/ml_methods/__init__.py
immuneML/ml_methods/classifiers/AtchleyKmerMILClassifier.py
immuneML/ml_methods/classifiers/BinaryFeatureClassifier.py
immuneML/ml_methods/classifiers/DeepRC.py
immuneML/ml_methods/classifiers/GradientBoosting.py
immuneML/ml_methods/classifiers/KNN.py
immuneML/ml_methods/classifiers/KerasSequenceCNN.py
immuneML/ml_methods/classifiers/LogRegressionCustomPenalty.py
immuneML/ml_methods/classifiers/LogisticRegression.py
immuneML/ml_methods/classifiers/MLMethod.py
immuneML/ml_methods/classifiers/PrecomputedKNN.py
immuneML/ml_methods/classifiers/ProbabilisticBinaryClassifier.py
immuneML/ml_methods/classifiers/RandomForestClassifier.py
immuneML/ml_methods/classifiers/ReceptorCNN.py
immuneML/ml_methods/classifiers/SVC.py
immuneML/ml_methods/classifiers/SVM.py
immuneML/ml_methods/classifiers/SklearnMethod.py
immuneML/ml_methods/classifiers/TCRdistClassifier.py
immuneML/ml_methods/classifiers/__init__.py
immuneML/ml_methods/clustering/AgglomerativeClustering.py
immuneML/ml_methods/clustering/ClusteringMethod.py
immuneML/ml_methods/clustering/DBSCAN.py
immuneML/ml_methods/clustering/HDBSCAN.py
immuneML/ml_methods/clustering/KMeans.py
immuneML/ml_methods/clustering/__init__.py
immuneML/ml_methods/dim_reduction/DimRedMethod.py
immuneML/ml_methods/dim_reduction/KernelPCA.py
immuneML/ml_methods/dim_reduction/PCA.py
immuneML/ml_methods/dim_reduction/TSNE.py
immuneML/ml_methods/dim_reduction/UMAP.py
immuneML/ml_methods/dim_reduction/__init__.py
immuneML/ml_methods/generative_models/BackgroundSequences.py
immuneML/ml_methods/generative_models/ExperimentalImport.py
immuneML/ml_methods/generative_models/GenerativeModel.py
immuneML/ml_methods/generative_models/InternalOlgaModel.py
immuneML/ml_methods/generative_models/KLEvaluator.py
immuneML/ml_methods/generative_models/MultinomialKmerModel.py
immuneML/ml_methods/generative_models/OLGA.py
immuneML/ml_methods/generative_models/PWM.py
immuneML/ml_methods/generative_models/ProGen.py
immuneML/ml_methods/generative_models/SequenceTransitionDistribution.py
immuneML/ml_methods/generative_models/SimpleLSTM.py
immuneML/ml_methods/generative_models/SimpleVAE.py
immuneML/ml_methods/generative_models/SoNNia.py
immuneML/ml_methods/generative_models/__init__.py
immuneML/ml_methods/generative_models/progen/ProGenConfig.py
immuneML/ml_methods/generative_models/progen/ProGenForCausalLM.py
immuneML/ml_methods/generative_models/progen/__init__.py
immuneML/ml_methods/helper_methods/FurthestNeighborClassifier.py
immuneML/ml_methods/helper_methods/__init__.py
immuneML/ml_methods/pytorch_implementations/PyTorchLogisticRegression.py
immuneML/ml_methods/pytorch_implementations/PyTorchReceptorCNN.py
immuneML/ml_methods/pytorch_implementations/SimpleLSTMGenerator.py
immuneML/ml_methods/pytorch_implementations/SimpleVAEGenerator.py
immuneML/ml_methods/pytorch_implementations/__init__.py
immuneML/ml_methods/util/Util.py
immuneML/ml_methods/util/__init__.py
immuneML/ml_methods/util/pytorch_util.py
immuneML/ml_metrics/ClassificationMetric.py
immuneML/ml_metrics/ClusteringMetric.py
immuneML/ml_metrics/MetricUtil.py
immuneML/ml_metrics/__init__.py
immuneML/ml_metrics/ml_metrics.py
immuneML/pairwise_repertoire_comparison/ComparisonData.py
immuneML/pairwise_repertoire_comparison/ComparisonDataBatch.py
immuneML/pairwise_repertoire_comparison/PairwiseRepertoireComparison.py
immuneML/pairwise_repertoire_comparison/__init__.py
immuneML/preprocessing/Preprocessor.py
immuneML/preprocessing/ReferenceSequenceAnnotator.py
immuneML/preprocessing/SubjectRepertoireCollector.py
immuneML/preprocessing/__init__.py
immuneML/preprocessing/filters/ChainRepertoireFilter.py
immuneML/preprocessing/filters/ClonesPerRepertoireFilter.py
immuneML/preprocessing/filters/CountAggregationFunction.py
immuneML/preprocessing/filters/CountPerSequenceFilter.py
immuneML/preprocessing/filters/DuplicateSequenceFilter.py
immuneML/preprocessing/filters/Filter.py
immuneML/preprocessing/filters/MetadataFilter.py
immuneML/preprocessing/filters/SequenceLengthFilter.py
immuneML/preprocessing/filters/__init__.py
immuneML/presentation/InstructionPresentation.py
immuneML/presentation/PresentationFactory.py
immuneML/presentation/PresentationFormat.py
immuneML/presentation/TemplateParser.py
immuneML/presentation/__init__.py
immuneML/presentation/html/ClusteringHTMLBuilder.py
immuneML/presentation/html/DatasetExportHTMLBuilder.py
immuneML/presentation/html/ExploratoryAnalysisHTMLBuilder.py
immuneML/presentation/html/FailedGalaxyHTMLBuilder.py
immuneML/presentation/html/FeasibilitySummaryHTMLBuilder.py
immuneML/presentation/html/GenModelHTMLBuilder.py
immuneML/presentation/html/HPHTMLBuilder.py
immuneML/presentation/html/HTMLBuilder.py
immuneML/presentation/html/LIgOSimulationHTMLBuilder.py
immuneML/presentation/html/MLApplicationHTMLBuilder.py
immuneML/presentation/html/MultiDatasetBenchmarkHTMLBuilder.py
immuneML/presentation/html/SubsamplingHTMLBuilder.py
immuneML/presentation/html/Util.py
immuneML/presentation/html/__init__.py
immuneML/presentation/html/templates/AssessmentSplitDetails.html
immuneML/presentation/html/templates/Clustering.html
immuneML/presentation/html/templates/ClusteringSettingDetails.html
immuneML/presentation/html/templates/ClusteringSplit.html
immuneML/presentation/html/templates/DatasetExport.html
immuneML/presentation/html/templates/ExploratoryAnalysis.html
immuneML/presentation/html/templates/FailedGalaxy.html
immuneML/presentation/html/templates/FeasibilitySummary.html
immuneML/presentation/html/templates/GenModel.html
immuneML/presentation/html/templates/HPOptimization.html
immuneML/presentation/html/templates/MLApplication.html
immuneML/presentation/html/templates/MLTraining.html
immuneML/presentation/html/templates/MultiDatasetBenchmark.html
immuneML/presentation/html/templates/Reports.html
immuneML/presentation/html/templates/SelectionDetails.html
immuneML/presentation/html/templates/Simulation.html
immuneML/presentation/html/templates/Subsampling.html
immuneML/presentation/html/templates/index.html
immuneML/presentation/html/templates/css/custom.css
immuneML/reports/PlotlyUtil.py
immuneML/reports/Report.py
immuneML/reports/ReportOutput.py
immuneML/reports/ReportResult.py
immuneML/reports/ReportUtil.py
immuneML/reports/__init__.py
immuneML/reports/clustering_method_reports/ClusteringMethodReport.py
immuneML/reports/clustering_method_reports/ClusteringVisualization.py
immuneML/reports/clustering_method_reports/Dendrogram.py
immuneML/reports/clustering_method_reports/ExternalLabelClusterSummary.py
immuneML/reports/clustering_method_reports/__init__.py
immuneML/reports/clustering_reports/ClusteringReport.py
immuneML/reports/clustering_reports/ClusteringStabilityReport.py
immuneML/reports/clustering_reports/ExternalLabelMetricHeatmap.py
immuneML/reports/clustering_reports/__init__.py
immuneML/reports/data_reports/AminoAcidFrequencyDistribution.py
immuneML/reports/data_reports/CompAIRRClusteringReport.py
immuneML/reports/data_reports/DataReport.py
immuneML/reports/data_reports/GLIPH2Exporter.py
immuneML/reports/data_reports/LabelDist.py
immuneML/reports/data_reports/LabelOverlap.py
immuneML/reports/data_reports/MotifGeneralizationAnalysis.py
immuneML/reports/data_reports/NodeDegreeDistribution.py
immuneML/reports/data_reports/RecoveredSignificantFeatures.py
immuneML/reports/data_reports/RepertoireClonotypeSummary.py
immuneML/reports/data_reports/SequenceCountDistribution.py
immuneML/reports/data_reports/SequenceLengthDistribution.py
immuneML/reports/data_reports/SequencesWithSignificantKmers.py
immuneML/reports/data_reports/ShannonDiversityOverview.py
immuneML/reports/data_reports/SignificantFeatures.py
immuneML/reports/data_reports/SignificantKmerPositions.py
immuneML/reports/data_reports/TrueMotifsSummaryBarplot.py
immuneML/reports/data_reports/VJGeneDistribution.py
immuneML/reports/data_reports/__init__.py
immuneML/reports/encoding_reports/DesignMatrixExporter.py
immuneML/reports/encoding_reports/DimensionalityReduction.py
immuneML/reports/encoding_reports/EncodingReport.py
immuneML/reports/encoding_reports/FeatureComparison.py
immuneML/reports/encoding_reports/FeatureDistribution.py
immuneML/reports/encoding_reports/FeatureReport.py
immuneML/reports/encoding_reports/FeatureValueBarplot.py
immuneML/reports/encoding_reports/GroundTruthMotifOverlap.py
immuneML/reports/encoding_reports/Matches.py
immuneML/reports/encoding_reports/MotifTestSetPerformance.py
immuneML/reports/encoding_reports/NonMotifSequenceSimilarity.py
immuneML/reports/encoding_reports/PositionalMotifFrequencies.py
immuneML/reports/encoding_reports/RelevantSequenceExporter.py
immuneML/reports/encoding_reports/__init__.py
immuneML/reports/gen_model_reports/GenModelReport.py
immuneML/reports/gen_model_reports/PWMSummary.py
immuneML/reports/gen_model_reports/VAESummary.py
immuneML/reports/gen_model_reports/__init__.py
immuneML/reports/ml_reports/BinaryFeaturePrecisionRecall.py
immuneML/reports/ml_reports/CoefficientPlottingSetting.py
immuneML/reports/ml_reports/CoefficientPlottingSettingList.py
immuneML/reports/ml_reports/Coefficients.py
immuneML/reports/ml_reports/ConfounderAnalysis.py
immuneML/reports/ml_reports/ConfusionMatrix.py
immuneML/reports/ml_reports/DeepRCMotifDiscovery.py
immuneML/reports/ml_reports/KernelSequenceLogo.py
immuneML/reports/ml_reports/MLReport.py
immuneML/reports/ml_reports/MotifSeedRecovery.py
immuneML/reports/ml_reports/ROCCurve.py
immuneML/reports/ml_reports/SequenceAssociationLikelihood.py
immuneML/reports/ml_reports/TCRdistMotifDiscovery.py
immuneML/reports/ml_reports/TrainingPerformance.py
immuneML/reports/ml_reports/__init__.py
immuneML/reports/multi_dataset_reports/DiseaseAssociatedSequenceOverlap.py
immuneML/reports/multi_dataset_reports/MultiDatasetReport.py
immuneML/reports/multi_dataset_reports/PerformanceOverview.py
immuneML/reports/multi_dataset_reports/__init__.py
immuneML/reports/train_gen_model_reports/KLKmerComparison.py
immuneML/reports/train_gen_model_reports/TrainGenModelReport.py
immuneML/reports/train_gen_model_reports/__init__.py
immuneML/reports/train_ml_model_reports/CVFeaturePerformance.py
immuneML/reports/train_ml_model_reports/DiseaseAssociatedSequenceCVOverlap.py
immuneML/reports/train_ml_model_reports/MLSettingsPerformance.py
immuneML/reports/train_ml_model_reports/PerformancePerLabel.py
immuneML/reports/train_ml_model_reports/ROCCurveSummary.py
immuneML/reports/train_ml_model_reports/ReferenceSequenceOverlap.py
immuneML/reports/train_ml_model_reports/TrainMLModelReport.py
immuneML/reports/train_ml_model_reports/__init__.py
immuneML/simulation/LigoSimState.py
immuneML/simulation/SimConfig.py
immuneML/simulation/SimConfigItem.py
immuneML/simulation/__init__.py
immuneML/simulation/dataset_generation/RandomDatasetGenerator.py
immuneML/simulation/dataset_generation/__init__.py
immuneML/simulation/implants/ImplantAnnotation.py
immuneML/simulation/implants/LigoPWM.py
immuneML/simulation/implants/Motif.py
immuneML/simulation/implants/MotifInstance.py
immuneML/simulation/implants/SeedMotif.py
immuneML/simulation/implants/Signal.py
immuneML/simulation/implants/__init__.py
immuneML/simulation/simulation_strategy/ImplantingStrategy.py
immuneML/simulation/simulation_strategy/RejectionSamplingStrategy.py
immuneML/simulation/simulation_strategy/SimulationStrategy.py
immuneML/simulation/simulation_strategy/__init__.py
immuneML/simulation/util/__init__.py
immuneML/simulation/util/bnp_util.py
immuneML/simulation/util/igor_helper.py
immuneML/simulation/util/signal_annotation.py
immuneML/simulation/util/util.py
immuneML/util/AdaptiveImportHelper.py
immuneML/util/CompAIRRHelper.py
immuneML/util/CompAIRRParams.py
immuneML/util/DistanceMetrics.py
immuneML/util/DocEnumHelper.py
immuneML/util/EncoderHelper.py
immuneML/util/ExporterHelper.py
immuneML/util/FilenameHandler.py
immuneML/util/ImportHelper.py
immuneML/util/KmerHelper.py
immuneML/util/Logger.py
immuneML/util/MotifPerformancePlotHelper.py
immuneML/util/NameBuilder.py
immuneML/util/NumpyHelper.py
immuneML/util/ParameterValidator.py
immuneML/util/PathBuilder.py
immuneML/util/PositionHelper.py
immuneML/util/ReadsType.py
immuneML/util/ReflectionHandler.py
immuneML/util/RepertoireBuilder.py
immuneML/util/SequenceAnalysisHelper.py
immuneML/util/SignificantFeaturesHelper.py
immuneML/util/StringHelper.py
immuneML/util/TCRdistHelper.py
immuneML/util/__init__.py
immuneML/workflows/__init__.py
immuneML/workflows/instructions/Instruction.py
immuneML/workflows/instructions/MLProcess.py
immuneML/workflows/instructions/TrainMLModelInstruction.py
immuneML/workflows/instructions/__init__.py
immuneML/workflows/instructions/quickstart.py
immuneML/workflows/instructions/apply_gen_model/ApplyGenModelInstruction.py
immuneML/workflows/instructions/apply_gen_model/__init__.py
immuneML/workflows/instructions/clustering/ClusteringInstruction.py
immuneML/workflows/instructions/clustering/ClusteringReportHandler.py
immuneML/workflows/instructions/clustering/ClusteringRunner.py
immuneML/workflows/instructions/clustering/ClusteringState.py
immuneML/workflows/instructions/clustering/ValidationHandler.py
immuneML/workflows/instructions/clustering/__init__.py
immuneML/workflows/instructions/clustering/clustering_run_model.py
immuneML/workflows/instructions/dataset_generation/DatasetExportInstruction.py
immuneML/workflows/instructions/dataset_generation/DatasetExportState.py
immuneML/workflows/instructions/dataset_generation/__init__.py
immuneML/workflows/instructions/exploratory_analysis/ExploratoryAnalysisInstruction.py
immuneML/workflows/instructions/exploratory_analysis/ExploratoryAnalysisState.py
immuneML/workflows/instructions/exploratory_analysis/ExploratoryAnalysisUnit.py
immuneML/workflows/instructions/exploratory_analysis/__init__.py
immuneML/workflows/instructions/ligo_sim_feasibility/FeasibilitySummaryInstruction.py
immuneML/workflows/instructions/ligo_sim_feasibility/__init__.py
immuneML/workflows/instructions/ligo_sim_feasibility/feasibility_reports.py
immuneML/workflows/instructions/ligo_simulation/LigoSimInstruction.py
immuneML/workflows/instructions/ligo_simulation/__init__.py
immuneML/workflows/instructions/ligo_simulation/runtime_reports.py
immuneML/workflows/instructions/ml_model_application/MLApplicationInstruction.py
immuneML/workflows/instructions/ml_model_application/MLApplicationState.py
immuneML/workflows/instructions/ml_model_application/__init__.py
immuneML/workflows/instructions/subsampling/SubsamplingInstruction.py
immuneML/workflows/instructions/subsampling/SubsamplingState.py
immuneML/workflows/instructions/subsampling/__init__.py
immuneML/workflows/instructions/train_gen_model/TrainGenModelInstruction.py
immuneML/workflows/instructions/train_gen_model/__init__.py
immuneML/workflows/steps/DataEncoder.py
immuneML/workflows/steps/DataEncoderParams.py
immuneML/workflows/steps/DataWeighter.py
immuneML/workflows/steps/DataWeighterParams.py
immuneML/workflows/steps/MLMethodAssessment.py
immuneML/workflows/steps/MLMethodAssessmentParams.py
immuneML/workflows/steps/MLMethodTrainer.py
immuneML/workflows/steps/MLMethodTrainerParams.py
immuneML/workflows/steps/Step.py
immuneML/workflows/steps/StepParams.py
immuneML/workflows/steps/__init__.py
immuneML/workflows/steps/data_splitter/DataSplitter.py
immuneML/workflows/steps/data_splitter/DataSplitterParams.py
immuneML/workflows/steps/data_splitter/LeaveOneOutSplitter.py
immuneML/workflows/steps/data_splitter/ManualSplitter.py
immuneML/workflows/steps/data_splitter/Util.py
immuneML/workflows/steps/data_splitter/__init__.py
scripts/DocumentatonFormat.py
scripts/__init__.py
scripts/check_new_encoder.py
scripts/check_new_ml_method.py
scripts/checker_util.py
scripts/specification_util.py
scripts/specs_docs_generation.py
useful_yaml_scipts/expand_ref_seq_sets.py
useful_yaml_scipts/run_all_yamls_in_dir.py