Index

_

__init__() (immuneML.reports.data_reports.DataReport.DataReport method) (immuneML.reports.encoding_reports.EncodingReport.EncodingReport method) (immuneML.reports.ml_reports.MLReport.MLReport method) (immuneML.reports.multi_dataset_reports.MultiDatasetReport.MultiDatasetReport method) (immuneML.reports.train_ml_model_reports.TrainMLModelReport.TrainMLModelReport method)

A

AbundanceEncoderHelper (class in immuneML.encodings.abundance_encoding.AbundanceEncoderHelper) AdaptiveImportHelper (class in immuneML.util.AdaptiveImportHelper) add() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) add_by_key() (immuneML.caching.CacheHandler.CacheHandler static method) add_cdr3_from_junction() (immuneML.util.ImportHelper.ImportHelper static method) add_default_allele_to_v_gene() (immuneML.util.TCRdistHelper.TCRdistHelper static method) add_default_fields_for_airr_seq_set() (immuneML.util.ImportHelper.ImportHelper static method) add_diagonal() (immuneML.reports.encoding_reports.FeatureComparison.FeatureComparison method) add_items_for_repertoire() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) add_label() (immuneML.environment.LabelConfiguration.LabelConfiguration method) add_single_axis_labels() (immuneML.reports.PlotlyUtil.PlotlyUtil static method) AIRRExporter (class in immuneML.IO.dataset_export.AIRRExporter) AIRRImport (class in immuneML.IO.dataset_import.AIRRImport) ALL (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) (immuneML.util.ReadsType.ReadsType attribute) all_direct_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method) all_nonabstract_subclass_basic_names() (immuneML.util.ReflectionHandler.ReflectionHandler static method) all_nonabstract_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method) all_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method) ALLELE_DELIMITER (immuneML.environment.Constants.Constants attribute) AMINO_ACID (immuneML.environment.SequenceType.SequenceType attribute) AminoAcidFrequencyDistribution (class in immuneML.reports.data_reports.AminoAcidFrequencyDistribution)

AND (immuneML.analysis.criteria_matches.BooleanType.BooleanType attribute) annotate_sequences() (in module immuneML.simulation.util.util) annotation_fields (immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction.LigoSimInstruction property) apply_with_weights() (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) assert_all_in_valid_list() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_all_type_and_value() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_any_value_present() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_in_valid_list() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_keys() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_keys_present() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_region_type() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_sequence_type() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_type_and_value() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_valid_tabular_file() (immuneML.util.ParameterValidator.ParameterValidator static method) assess_performance() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) assessment (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) assessment_states (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) assign_duplicate_counts() (in module immuneML.simulation.util.util) ATCHLEY_FACTOR_COUNT (immuneML.encodings.atchley_kmer_encoding.Util.Util attribute) ATCHLEY_FACTORS (immuneML.encodings.atchley_kmer_encoding.Util.Util attribute) AtchleyKmerEncoder (class in immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder) AtchleyKmerMILClassifier (class in immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier) AVG (immuneML.analysis.data_manipulation.ReductionMethod.ReductionMethod attribute) AxisType (class in immuneML.analysis.AxisType)

B

binarize_label_classes() (immuneML.ml_methods.util.Util.Util static method) BINARY (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) BooleanType (class in immuneML.analysis.criteria_matches.BooleanType) build() (immuneML.presentation.html.DatasetExportHTMLBuilder.DatasetExportHTMLBuilder static method) (immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder.ExploratoryAnalysisHTMLBuilder static method) (immuneML.presentation.html.HPHTMLBuilder.HPHTMLBuilder static method) (immuneML.presentation.html.HTMLBuilder.HTMLBuilder static method) (immuneML.presentation.html.MLApplicationHTMLBuilder.MLApplicationHTMLBuilder static method) (immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder.MultiDatasetBenchmarkHTMLBuilder static method) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder static method) (immuneML.util.PathBuilder.PathBuilder static method) (immuneML.util.RepertoireBuilder.RepertoireBuilder static method) build_abundance_matrix() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) build_comparison_data() (immuneML.util.EncoderHelper.EncoderHelper static method) build_comparison_params() (immuneML.util.EncoderHelper.EncoderHelper static method) build_dataset() (immuneML.util.RepertoireBuilder.RepertoireBuilder static method) build_distance_matrix() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) build_imgt_positions() (in module immuneML.simulation.util.util) build_labels() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) build_name_from_dict() (immuneML.util.NameBuilder.NameBuilder static method) build_object() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder static method) (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder static method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder static method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder static method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method) (immuneML.encodings.distance_encoding.TCRdistEncoder.TCRdistEncoder static method) (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder static method) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder static method) (immuneML.encodings.onehot.OneHotEncoder.OneHotEncoder static method) (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder static method) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder static method) (immuneML.encodings.reference_encoding.MatchedSequencesEncoder.MatchedSequencesEncoder static method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder static method) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams class method) (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport class method) (immuneML.ml_methods.generative_models.OLGA.OLGA class method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter class method) (immuneML.preprocessing.filters.SequenceLengthFilter.SequenceLengthFilter class method) (immuneML.preprocessing.ReferenceSequenceAnnotator.ReferenceSequenceAnnotator class method) (immuneML.reports.data_reports.AminoAcidFrequencyDistribution.AminoAcidFrequencyDistribution class method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter class method) (immuneML.reports.data_reports.ReceptorDatasetOverview.ReceptorDatasetOverview class method) (immuneML.reports.data_reports.RecoveredSignificantFeatures.RecoveredSignificantFeatures class method) (immuneML.reports.data_reports.RepertoireClonotypeSummary.RepertoireClonotypeSummary class method) (immuneML.reports.data_reports.SequenceLengthDistribution.SequenceLengthDistribution class method) (immuneML.reports.data_reports.SequencesWithSignificantKmers.SequencesWithSignificantKmers class method) (immuneML.reports.data_reports.SignificantFeatures.SignificantFeatures class method) (immuneML.reports.data_reports.SignificantKmerPositions.SignificantKmerPositions class method) (immuneML.reports.data_reports.SimpleDatasetOverview.SimpleDatasetOverview class method) (immuneML.reports.encoding_reports.DesignMatrixExporter.DesignMatrixExporter class method) (immuneML.reports.encoding_reports.FeatureComparison.FeatureComparison class method) (immuneML.reports.encoding_reports.FeatureDistribution.FeatureDistribution class method) (immuneML.reports.encoding_reports.FeatureValueBarplot.FeatureValueBarplot class method) (immuneML.reports.encoding_reports.Matches.Matches class method) (immuneML.reports.encoding_reports.RelevantSequenceExporter.RelevantSequenceExporter class method) (immuneML.reports.gen_model_reports.VAESummary.VAESummary class method) (immuneML.reports.ml_reports.Coefficients.Coefficients class method) (immuneML.reports.ml_reports.ConfounderAnalysis.ConfounderAnalysis class method) (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery class method) (immuneML.reports.ml_reports.KernelSequenceLogo.KernelSequenceLogo class method) (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery class method) (immuneML.reports.ml_reports.ROCCurve.ROCCurve class method) (immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood class method) (immuneML.reports.ml_reports.TCRdistMotifDiscovery.TCRdistMotifDiscovery class method) (immuneML.reports.ml_reports.TrainingPerformance.TrainingPerformance class method) (immuneML.reports.multi_dataset_reports.DiseaseAssociatedSequenceOverlap.DiseaseAssociatedSequenceOverlap class method) (immuneML.reports.multi_dataset_reports.PerformanceOverview.PerformanceOverview class method) (immuneML.reports.Report.Report class method) (immuneML.reports.train_ml_model_reports.CVFeaturePerformance.CVFeaturePerformance class method) (immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap.DiseaseAssociatedSequenceCVOverlap class method) (immuneML.reports.train_ml_model_reports.MLSettingsPerformance.MLSettingsPerformance class method) (immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap.ReferenceSequenceOverlap class method) (immuneML.reports.train_ml_model_reports.ROCCurveSummary.ROCCurveSummary class method)

build_path() (immuneML.workflows.instructions.quickstart.Quickstart method) build_reports() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method)

C

CACHE_PATH (immuneML.environment.Constants.Constants attribute) cache_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) CACHE_TYPE (immuneML.environment.Constants.Constants attribute) CacheHandler (class in immuneML.caching.CacheHandler) CacheObjectType (class in immuneML.caching.CacheObjectType) CacheType (class in immuneML.caching.CacheType) calculate_seed_overlap() (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) camel_case_to_word_string() (immuneML.util.StringHelper.StringHelper static method) camel_case_to_words() (immuneML.util.StringHelper.StringHelper static method) can_compute_p_gens() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) can_fit_with_example_weights() (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.KNN.KNN method) (immuneML.ml_methods.classifiers.LogisticRegression.LogisticRegression method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.RandomForestClassifier.RandomForestClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SVC.SVC method) (immuneML.ml_methods.classifiers.SVM.SVM method) (immuneML.ml_methods.classifiers.TCRdistClassifier.TCRdistClassifier method) can_generate_from_skewed_gene_models() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) can_predict_proba() (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.KNN.KNN method) (immuneML.ml_methods.classifiers.LogisticRegression.LogisticRegression method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.RandomForestClassifier.RandomForestClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.classifiers.SVC.SVC method) (immuneML.ml_methods.classifiers.SVM.SVM method) (immuneML.ml_methods.classifiers.TCRdistClassifier.TCRdistClassifier method) ChainRepertoireFilter (class in immuneML.preprocessing.filters.ChainRepertoireFilter) check() (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) check_clonal_frequency() (in module immuneML.dsl.definition_parsers.SignalParser) check_compairr_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) check_dataset_not_empty() (immuneML.preprocessing.filters.Filter.Filter method) check_dataset_type() (immuneML.preprocessing.Preprocessor.Preprocessor method) check_dataset_type_available_in_mapping() (immuneML.util.EncoderHelper.EncoderHelper static method) check_encoder_compatibility() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) check_export_format() (immuneML.api.galaxy.Util.Util static method) check_instruction_type() (immuneML.api.galaxy.Util.Util static method) check_is_fitted() (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) check_is_positive_class() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) check_iteration_progress() (in module immuneML.simulation.util.util) check_keys() (immuneML.dsl.ImmuneMLParser.ImmuneMLParser static method) check_label_format() (immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper static method) check_or_discover_metadata_file() (immuneML.IO.dataset_import.DataImport.DataImport method) check_parameters() (immuneML.api.galaxy.Util.Util static method) check_paths() (immuneML.api.galaxy.Util.Util static method) check_positive_class_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) check_prerequisites() (immuneML.reports.data_reports.AminoAcidFrequencyDistribution.AminoAcidFrequencyDistribution method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter method) (immuneML.reports.data_reports.ReceptorDatasetOverview.ReceptorDatasetOverview method) (immuneML.reports.data_reports.RecoveredSignificantFeatures.RecoveredSignificantFeatures method) (immuneML.reports.data_reports.RepertoireClonotypeSummary.RepertoireClonotypeSummary method) (immuneML.reports.data_reports.SequenceLengthDistribution.SequenceLengthDistribution method) (immuneML.reports.data_reports.SequencesWithSignificantKmers.SequencesWithSignificantKmers method) (immuneML.reports.data_reports.SignificantFeatures.SignificantFeatures method) (immuneML.reports.data_reports.SignificantKmerPositions.SignificantKmerPositions method) (immuneML.reports.encoding_reports.DesignMatrixExporter.DesignMatrixExporter method) (immuneML.reports.encoding_reports.FeatureComparison.FeatureComparison method) (immuneML.reports.encoding_reports.FeatureReport.FeatureReport method) (immuneML.reports.encoding_reports.Matches.Matches method) (immuneML.reports.encoding_reports.RelevantSequenceExporter.RelevantSequenceExporter method) (immuneML.reports.gen_model_reports.VAESummary.VAESummary method) (immuneML.reports.ml_reports.Coefficients.Coefficients method) (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery method) (immuneML.reports.ml_reports.KernelSequenceLogo.KernelSequenceLogo method) (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) (immuneML.reports.ml_reports.ROCCurve.ROCCurve method) (immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood method) (immuneML.reports.ml_reports.TCRdistMotifDiscovery.TCRdistMotifDiscovery method) (immuneML.reports.ml_reports.TrainingPerformance.TrainingPerformance method) (immuneML.reports.Report.Report method) (immuneML.reports.train_ml_model_reports.CVFeaturePerformance.CVFeaturePerformance method) (immuneML.reports.train_ml_model_reports.MLSettingsPerformance.MLSettingsPerformance method) (immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap.ReferenceSequenceOverlap method)

check_sequence_count() (in module immuneML.simulation.util.util) check_sim_strategy_setup() (in module immuneML.dsl.definition_parsers.SimulationParser) choose_implant_position() (in module immuneML.simulation.util.util) CLASSIFICATION (immuneML.environment.LabelType.LabelType attribute) clear_cache() (immuneML.app.ImmuneMLApp.ImmuneMLApp method) clonal_frequency (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) CLONAL_PERCENTAGE (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) clone() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) (immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy.HPOptimizationStrategy method) ClonesPerRepertoireFilter (class in immuneML.preprocessing.filters.ClonesPerRepertoireFilter) CODON_TABLE (immuneML.IO.dataset_import.IGoRImport.IGoRImport attribute) CoefficientPlottingSetting (class in immuneML.reports.ml_reports.CoefficientPlottingSetting) CoefficientPlottingSettingList (class in immuneML.reports.ml_reports.CoefficientPlottingSettingList) Coefficients (class in immuneML.reports.ml_reports.Coefficients) COLUMN (immuneML.analysis.criteria_matches.DataType.DataType attribute) column_mapping (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) column_mapping_synonyms (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) columns_to_load (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) combined_dataset (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) COMMENT_SIGN (immuneML.environment.Constants.Constants attribute) compairr_path (immuneML.util.CompAIRRParams.CompAIRRParams attribute) compairr_paths (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) CompAIRRBatchIterator (class in immuneML.encodings.abundance_encoding.CompAIRRBatchIterator) CompAIRRDistanceEncoder (class in immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder) CompAIRRHelper (class in immuneML.util.CompAIRRHelper) CompAIRRParams (class in immuneML.util.CompAIRRParams) CompAIRRSequenceAbundanceEncoder (class in immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder) compare() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) compare_repertoires() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) ComparisonData (class in immuneML.pairwise_repertoire_comparison.ComparisonData) ComparisonDataBatch (class in immuneML.pairwise_repertoire_comparison.ComparisonDataBatch) COMPATIBLE_ENCODERS (immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap.DiseaseAssociatedSequenceCVOverlap attribute) compute_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_contributions() (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery method) compute_overlap_matrix() (immuneML.util.SequenceAnalysisHelper.SequenceAnalysisHelper static method) compute_p_gen() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) compute_p_gens() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) compute_relative_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_sequence_count() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) compute_tcr_dist() (immuneML.util.TCRdistHelper.TCRdistHelper static method) compute_tcrb_relative_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) ConfounderAnalysis (class in immuneML.reports.ml_reports.ConfounderAnalysis) Constants (class in immuneML.environment.Constants) construct_sequence_metadata_object() (in module immuneML.simulation.util.util) contains() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) context (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) CONTINUOUS_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) convert_to_snake_case() (immuneML.dsl.DefaultParamsLoader.DefaultParamsLoader static method) CORES (immuneML.analysis.SequenceMatcher.SequenceMatcher attribute) COUNT (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) CountAggregationFunction (class in immuneML.preprocessing.filters.CountAggregationFunction) CountPerSequenceFilter (class in immuneML.preprocessing.filters.CountPerSequenceFilter) COUNTS_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) create_all_kmers() (immuneML.util.KmerHelper.KmerHelper static method) create_assessment_path() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) create_comparison_data() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) create_gapped_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_gapped_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_gapped_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_within_HD() (immuneML.util.KmerHelper.KmerHelper static method) create_label_config() (immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper static method) create_method_instance() (immuneML.dsl.definition_parsers.MLParser.MLParser static method) create_model() (immuneML.encodings.word2vec.model_creator.KmerPairModelCreator.KmerPairModelCreator method) (immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy.ModelCreatorStrategy method) (immuneML.encodings.word2vec.model_creator.SequenceModelCreator.SequenceModelCreator method) create_selection_path() (immuneML.hyperparameter_optimization.core.HPSelection.HPSelection static method) create_sentences_from_repertoire() (immuneML.util.KmerHelper.KmerHelper static method) create_specfication() (immuneML.workflows.instructions.quickstart.Quickstart method) CriteriaMatcher (class in immuneML.analysis.criteria_matches.CriteriaMatcher) CriteriaTypeInstantiator (class in immuneML.analysis.criteria_matches.CriteriaTypeInstantiator) CSS_PATH (immuneML.presentation.html.DatasetExportHTMLBuilder.DatasetExportHTMLBuilder attribute) (immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder.ExploratoryAnalysisHTMLBuilder attribute) (immuneML.presentation.html.HPHTMLBuilder.HPHTMLBuilder attribute) (immuneML.presentation.html.MLApplicationHTMLBuilder.MLApplicationHTMLBuilder attribute) (immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder.MultiDatasetBenchmarkHTMLBuilder attribute) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder attribute) custom_fields (immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction.LigoSimInstruction property) custom_func_keys (immuneML.dsl.definition_parsers.SignalParser.SignalParser attribute) CUTOFF (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) CVFeaturePerformance (class in immuneML.reports.train_ml_model_reports.CVFeaturePerformance)

D

DataEncoder (class in immuneML.workflows.steps.DataEncoder) DataEncoderParams (class in immuneML.workflows.steps.DataEncoderParams) DataExporter (class in immuneML.IO.dataset_export.DataExporter) DataImport (class in immuneML.IO.dataset_import.DataImport) DataReport (class in immuneML.reports.data_reports.DataReport) DataReshaper (class in immuneML.analysis.data_manipulation.DataReshaper) DATASET (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) dataset (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) (immuneML.workflows.steps.DataEncoderParams.DataEncoderParams attribute) dataset_exporters (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) dataset_file (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) DATASET_FORMAT (immuneML.util.ImportHelper.ImportHelper attribute) dataset_mapping (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder attribute) (immuneML.encodings.onehot.OneHotEncoder.OneHotEncoder attribute) (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder attribute) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder attribute) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder attribute) DatasetEncoder (class in immuneML.encodings.DatasetEncoder) DatasetExportHTMLBuilder (class in immuneML.presentation.html.DatasetExportHTMLBuilder) DatasetExportInstruction (class in immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction) DatasetExportParser (class in immuneML.dsl.instruction_parsers.DatasetExportParser) DatasetExportState (class in immuneML.workflows.instructions.dataset_generation.DatasetExportState) DatasetGenerationTool (class in immuneML.api.galaxy.DatasetGenerationTool) DatasetImportParams (class in immuneML.IO.dataset_import.DatasetImportParams) datasets (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) DataSimulationTool (class in immuneML.api.galaxy.DataSimulationTool) DataSplitter (class in immuneML.workflows.steps.data_splitter.DataSplitter) DataSplitterParams (class in immuneML.workflows.steps.data_splitter.DataSplitterParams) DataType (class in immuneML.analysis.criteria_matches.DataType) DeepRC (class in immuneML.ml_methods.classifiers.DeepRC) DeepRCEncoder (class in immuneML.encodings.deeprc.DeepRCEncoder)

DeepRCMotifDiscovery (class in immuneML.reports.ml_reports.DeepRCMotifDiscovery) default_analysis_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) DEFAULT_MODEL_FOLDER_MAP (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) default_model_name (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) default_parameters (immuneML.ml_methods.classifiers.LogisticRegression.LogisticRegression attribute) default_params_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) DefaultParamsLoader (class in immuneML.dsl.DefaultParamsLoader) DefinitionParser (class in immuneML.dsl.definition_parsers.DefinitionParser) DefinitionParserOutput (class in immuneML.dsl.definition_parsers.DefinitionParserOutput) DESCRIPTION_LABELS (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder attribute) DESCRIPTION_REPERTOIRES (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder attribute) DesignMatrixExporter (class in immuneML.reports.encoding_reports.DesignMatrixExporter) determine_compairr_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) differences (immuneML.util.CompAIRRParams.CompAIRRParams attribute) dim_reduction (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) discover_classes_by_partial_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) discover_dataset_path() (immuneML.api.galaxy.Util.Util static method) DiseaseAssociatedSequenceCVOverlap (class in immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap) DiseaseAssociatedSequenceOverlap (class in immuneML.reports.multi_dataset_reports.DiseaseAssociatedSequenceOverlap) DistanceEncoder (class in immuneML.encodings.distance_encoding.DistanceEncoder) DistanceMetricType (class in immuneML.encodings.distance_encoding.DistanceMetricType) DISTRIBUTION_PERCENTAGE_TO_SHOW (immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood attribute) do_repertoire_overlap (immuneML.util.CompAIRRParams.CompAIRRParams attribute) do_sequence_matching (immuneML.util.CompAIRRParams.CompAIRRParams attribute) DocEnumHelper (class in immuneML.util.DocEnumHelper) DOCS_TITLE (immuneML.ml_methods.classifiers.MLMethod.MLMethod attribute) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel attribute) (immuneML.reports.data_reports.DataReport.DataReport attribute) (immuneML.reports.encoding_reports.EncodingReport.EncodingReport attribute) (immuneML.reports.gen_model_reports.GenModelReport.GenModelReport attribute) (immuneML.reports.ml_reports.MLReport.MLReport attribute) (immuneML.reports.multi_dataset_reports.MultiDatasetReport.MultiDatasetReport attribute) (immuneML.reports.train_ml_model_reports.TrainMLModelReport.TrainMLModelReport attribute) drop_empty_sequences() (immuneML.util.ImportHelper.ImportHelper static method) drop_illegal_character_sequences() (immuneML.util.ImportHelper.ImportHelper static method) DuplicateSequenceFilter (class in immuneML.preprocessing.filters.DuplicateSequenceFilter)

E

encode() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) (immuneML.encodings.distance_encoding.TCRdistEncoder.TCRdistEncoder method) (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder method) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder method) (immuneML.encodings.onehot.OneHotEncoder.OneHotEncoder method) (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder method) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder method) (immuneML.encodings.reference_encoding.MatchedSequencesEncoder.MatchedSequencesEncoder method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) encode_dataset() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) encode_dataset_by_kmer_freq() (in module immuneML.api.api_encoding) encode_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_element_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_labels (immuneML.encodings.EncoderParams.EncoderParams attribute) encode_repertoire() (immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder.EvennessProfileRepertoireEncoder method) (immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder.KmerFreqRepertoireEncoder method) encode_repertoire_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_sequence() (immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder.GappedKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder.IdentitySequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder.IMGTGappedKmerEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder.IMGTKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder.KmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy.SequenceEncodingStrategy static method) encoder (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.steps.DataEncoderParams.DataEncoderParams attribute) encoder_params (immuneML.workflows.steps.DataEncoderParams.DataEncoderParams attribute) EncoderHelper (class in immuneML.util.EncoderHelper) EncoderParams (class in immuneML.encodings.EncoderParams) ENCODING (immuneML.caching.CacheObjectType.CacheObjectType attribute) (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) encoding_class (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) encoding_file (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) encoding_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) encoding_parameters (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) ENCODING_STEP (immuneML.caching.CacheObjectType.CacheObjectType attribute)

encoding_test_results (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) encoding_train_results (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) EncodingParser (class in immuneML.dsl.definition_parsers.EncodingParser) EncodingReport (class in immuneML.reports.encoding_reports.EncodingReport) EntropyCalculator (class in immuneML.analysis.entropy_calculations.EntropyCalculator) EnvironmentSettings (class in immuneML.environment.EnvironmentSettings) evaluate_and() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_column() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_greater_than() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_hp_setting() (immuneML.hyperparameter_optimization.core.HPSelection.HPSelection static method) evaluate_in() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_less_than() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_not_in() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_not_na() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_or() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_random_n() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) evaluate_top_n() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) EvennessProfileEncoder (class in immuneML.encodings.evenness_profile.EvennessProfileEncoder) EvennessProfileRepertoireEncoder (class in immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder) example_weighting (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) exists() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.util.ReflectionHandler.ReflectionHandler static method) ExperimentalImport (class in immuneML.ml_methods.generative_models.ExperimentalImport) exploratory_analysis_units (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) ExploratoryAnalysisHTMLBuilder (class in immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder) ExploratoryAnalysisInstruction (class in immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction) ExploratoryAnalysisParser (class in immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser) ExploratoryAnalysisState (class in immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState) ExploratoryAnalysisUnit (class in immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit) export() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) (immuneML.IO.dataset_export.DataExporter.DataExporter static method) (immuneML.IO.ml_method.MLExporter.MLExporter static method) export_all_ml_settings (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) export_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_dataset() (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) export_galaxy_dataset() (immuneML.api.galaxy.Util.Util static method) export_metadata_file() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) export_pairwise_comparison() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_repertoire_tsv_files() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) export_zip() (immuneML.IO.ml_method.MLExporter.MLExporter static method) exported_datasets (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) EXTENSION (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) extract_dict_columns() (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport method) extract_locus_from_data() (immuneML.util.ImportHelper.ImportHelper static method) extract_sequence_dataset_params() (immuneML.util.ImportHelper.ImportHelper static method)

F

f1_score_macro() (in module immuneML.ml_metrics.ml_metrics) f1_score_micro() (in module immuneML.ml_metrics.ml_metrics) f1_score_weighted() (in module immuneML.ml_metrics.ml_metrics) FeasibilitySummaryInstruction (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FeasibilitySummaryState (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FeasibilitySumReports (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FEATURE_DELIMITER (immuneML.environment.Constants.Constants attribute) FeatureComparison (class in immuneML.reports.encoding_reports.FeatureComparison) FeatureDistribution (class in immuneML.reports.encoding_reports.FeatureDistribution) FeatureReport (class in immuneML.reports.encoding_reports.FeatureReport) FEATURES (immuneML.analysis.AxisType.AxisType attribute) FeatureScaler (class in immuneML.encodings.preprocessing.FeatureScaler) FeatureValueBarplot (class in immuneML.reports.encoding_reports.FeatureValueBarplot) fieldnames (immuneML.workflows.steps.MLMethodAssessment.MLMethodAssessment attribute) FilenameHandler (class in immuneML.util.FilenameHandler) Filter (class in immuneML.preprocessing.filters.Filter) filter_existing_items() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method)

filter_illegal_receptors() (immuneML.util.ImportHelper.ImportHelper static method) filter_illegal_sequences() (immuneML.util.ImportHelper.ImportHelper class method) filter_out_illegal_sequences() (in module immuneML.simulation.util.util) filter_sequences_by_length() (in module immuneML.simulation.util.util) FIRST (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) FIT (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod attribute) fit() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) fit_by_cross_validation() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) FIT_CV (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod attribute) formats (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) forward() (immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression.PyTorchLogisticRegression method) (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method)

G

GalaxyMLApplicationTool (class in immuneML.api.galaxy.GalaxyMLApplicationTool) GalaxySimulationTool (class in immuneML.api.galaxy.GalaxySimulationTool) GalaxyTool (class in immuneML.api.galaxy.GalaxyTool) GalaxyTrainMLModel (class in immuneML.api.galaxy.GalaxyTrainMLModel) GalaxyYamlTool (class in immuneML.api.galaxy.GalaxyYamlTool) GAP_LETTER (immuneML.environment.Constants.Constants attribute) GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) GappedKmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder) gen_examples_count (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) gen_imgt_positions_from_cdr3_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_junction_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_sequence() (immuneML.util.PositionHelper.PositionHelper static method) GENE_DELIMITER (immuneML.environment.Constants.Constants attribute) generate_cache_key() (immuneML.caching.CacheHandler.CacheHandler static method) generate_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) (immuneML.dsl.InstructionParser.InstructionParser static method) (immuneML.dsl.OutputParser.OutputParser static method) generate_from_skewed_gene_models() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) generate_next_setting() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) (immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy.HPOptimizationStrategy method) generate_random_metadata() (in module immuneML.api.api_encoding) generate_receptor_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_repertoire_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_report() (immuneML.reports.Report.Report method) generate_sequence_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_sequences() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) generated_dataset (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) GenerativeModel (class in immuneML.ml_methods.generative_models.GenerativeModel) GenericImport (class in immuneML.IO.dataset_import.GenericImport) GenModelReport (class in immuneML.reports.gen_model_reports.GenModelReport) genomic_data (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) get() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_additional_files() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder method) get_all_hps() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) (immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy.HPOptimizationStrategy method) get_all_motif_instances() (immuneML.simulation.implants.Signal.Signal method) get_all_params() (immuneML.dsl.ObjectParser.ObjectParser static method) get_all_possible_instances() (immuneML.simulation.implants.Motif.Motif method) get_allowed_positions() (in module immuneML.simulation.util.util) get_allowed_positions_for_annotation() (immuneML.util.PositionHelper.PositionHelper static method) get_alphabet() (immuneML.simulation.implants.Motif.Motif method) get_amino_acid_color_map() (immuneML.reports.PlotlyUtil.PlotlyUtil static method) get_atchely_factors() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) get_auxiliary_labels() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_average_performance() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) get_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_batch_dict() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_batch_from_path() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_batches() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_binary_negative_class() (immuneML.environment.Label.Label method) get_bnp_data() (in module immuneML.simulation.util.util) get_by_key() (immuneML.caching.CacheHandler.CacheHandler static method) get_by_type() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_cache_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_class() (immuneML.dsl.ObjectParser.ObjectParser static method) get_class_by_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_class_from_path() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_class_name() (immuneML.dsl.ObjectParser.ObjectParser static method) get_classes() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) get_classes_by_partial_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_cmd_args() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) get_compatible_encoders() (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.KNN.KNN method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.classifiers.TCRdistClassifier.TCRdistClassifier method) get_config() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_css_content() (immuneML.presentation.html.Util.Util static method) get_current_dataset() (immuneML.util.EncoderHelper.EncoderHelper static method) get_dataset_name() (immuneML.util.FilenameHandler.FilenameHandler static method) get_desc_for_storage() (immuneML.environment.Label.Label method) get_distribution_limits() (immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood method) get_documentation() (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder static method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder static method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder static method) (immuneML.hyperparameter_optimization.config.ReportConfig.ReportConfig static method) (immuneML.hyperparameter_optimization.config.SplitConfig.SplitConfig static method) (immuneML.IO.dataset_import.AIRRImport.AIRRImport static method) (immuneML.IO.dataset_import.GenericImport.GenericImport static method) (immuneML.IO.dataset_import.IGoRImport.IGoRImport static method) (immuneML.IO.dataset_import.ImmunoSEQRearrangementImport.ImmunoSEQRearrangementImport static method) (immuneML.IO.dataset_import.ImmunoSEQSampleImport.ImmunoSEQSampleImport static method) (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport static method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport static method) (immuneML.IO.dataset_import.TenxGenomicsImport.TenxGenomicsImport static method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) (immuneML.ml_methods.classifiers.KNN.KNN static method) (immuneML.ml_methods.classifiers.LogisticRegression.LogisticRegression static method) (immuneML.ml_methods.classifiers.PrecomputedKNN.PrecomputedKNN static method) (immuneML.ml_methods.classifiers.RandomForestClassifier.RandomForestClassifier static method) (immuneML.ml_methods.classifiers.SVC.SVC static method) (immuneML.ml_methods.classifiers.SVM.SVM static method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter static method) (immuneML.reports.ml_reports.Coefficients.Coefficients static method) (immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction.DatasetExportInstruction static method) (immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction.MLApplicationInstruction static method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction static method) (immuneML.workflows.instructions.TrainMLModelInstruction.TrainMLModelInstruction static method)

get_encoded_repertoire() (immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder.EvennessProfileRepertoireEncoder method) (immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder.KmerFreqRepertoireEncoder method) get_enum_names() (immuneML.util.DocEnumHelper.DocEnumHelper static method) get_enum_names_and_values() (immuneML.util.DocEnumHelper.DocEnumHelper static method) get_example_weights_by_identifiers() (immuneML.util.EncoderHelper.EncoderHelper static method) get_feature_names() (immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder.GappedKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder.IdentitySequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder.IMGTGappedKmerEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder.IMGTKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder.KmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy.SequenceEncodingStrategy static method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) get_file_path() (immuneML.caching.CacheHandler.CacheHandler static method) get_filename() (immuneML.util.FilenameHandler.FilenameHandler static method) get_full_specs_path() (immuneML.presentation.html.Util.Util static method) get_imgt_position_weights_for_annotation() (immuneML.util.PositionHelper.PositionHelper static method) get_imgt_position_weights_for_implanting() (immuneML.util.PositionHelper.PositionHelper static method) get_immuneML_version() (immuneML.ml_methods.util.Util.Util static method) get_item_names() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_item_vector() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_item_vectors() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_items() (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) get_j_genes() (immuneML.ml_methods.generative_models.SimpleVAE.PyTorchSequenceDataset method) get_key() (immuneML.hyperparameter_optimization.HPSetting.HPSetting method) get_keys_by_type() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_label_count() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_label_name() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) get_label_object() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_label_objects() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_label_values() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_labels_by_name() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_logfile_path() (immuneML.presentation.html.Util.Util static method) get_matching_func_for_repertoire() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) get_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) get_max_information_gain() (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method) get_max_length() (immuneML.simulation.implants.Motif.Motif method) get_max_seq_length() (in module immuneML.simulation.util.util) get_metric_fn() (immuneML.ml_metrics.MetricUtil.MetricUtil static method) get_min_seq_length() (in module immuneML.simulation.util.util) get_model_name() (immuneML.util.FilenameHandler.FilenameHandler static method) get_no_signal_sequences() (in module immuneML.simulation.util.util) get_numpy_representation() (immuneML.util.NumpyHelper.NumpyHelper static method) get_optimal_hps() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) (immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy.HPOptimizationStrategy method) get_package_info() (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) get_params() (immuneML.dsl.ObjectParser.ObjectParser static method) (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.KNN.KNN method) (immuneML.ml_methods.classifiers.LogisticRegression.LogisticRegression method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.RandomForestClassifier.RandomForestClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.classifiers.SVC.SVC method) (immuneML.ml_methods.classifiers.SVM.SVM method) (immuneML.ml_methods.classifiers.TCRdistClassifier.TCRdistClassifier method) get_performance() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) get_positive_class() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) get_receptor_filter_sort_kwargs() (immuneML.util.ImportHelper.ImportHelper static method) get_receptor_params() (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder method) get_region_type() (in module immuneML.simulation.util.util) get_relevant_sequence_attributes() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_relevant_sequence_indices() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) get_repertoire_contents() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) get_repertoire_filename_from_metadata_row() (immuneML.util.ImportHelper.ImportHelper static method) get_repertoire_vector() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_repertoire_vectors() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_seq_name_for_seq_object() (immuneML.encodings.EncoderParams.EncoderParams method) get_sequence_alphabet() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_sequence_field_name() (immuneML.encodings.EncoderParams.EncoderParams method) get_sequence_filenames() (immuneML.util.ImportHelper.ImportHelper static method) get_sequence_identifiers() (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) get_sequence_per_signal_count() (in module immuneML.simulation.util.util) get_sequence_set() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_sequence_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_sequence_vectors() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_signal_sequence_count() (in module immuneML.simulation.util.util) get_signal_sequences() (in module immuneML.simulation.util.util) get_signals() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_single_label_name_from_config() (immuneML.util.EncoderHelper.EncoderHelper static method) get_standardized_name() (immuneML.util.ImportHelper.ImportHelper static method) get_table_string_from_csv() (immuneML.presentation.html.Util.Util static method) get_table_string_from_csv_string() (immuneML.presentation.html.Util.Util static method) get_tmp_batches() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_train_val_indices() (immuneML.ml_methods.util.Util.Util static method) get_usage_documentation() (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod static method) get_v_genes() (immuneML.ml_methods.generative_models.SimpleVAE.PyTorchSequenceDataset method) GLIPH2Exporter (class in immuneML.reports.data_reports.GLIPH2Exporter) GREATER_THAN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) GridSearch (class in immuneML.hyperparameter_optimization.strategy.GridSearch) group_structured_array_by() (immuneML.util.NumpyHelper.NumpyHelper static method)

H

hamming_overlap() (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) hp_setting (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) hp_settings (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) hp_strategy (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) HPAssessment (class in immuneML.hyperparameter_optimization.core.HPAssessment) HPAssessmentState (class in immuneML.hyperparameter_optimization.states.HPAssessmentState) HPHTMLBuilder (class in immuneML.presentation.html.HPHTMLBuilder) HPItem (class in immuneML.hyperparameter_optimization.states.HPItem)

HPLabelState (class in immuneML.hyperparameter_optimization.states.HPLabelState) HPOptimizationStrategy (class in immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy) HPSelection (class in immuneML.hyperparameter_optimization.core.HPSelection) HPSelectionState (class in immuneML.hyperparameter_optimization.states.HPSelectionState) HPSetting (class in immuneML.hyperparameter_optimization.HPSetting) HPSettingResult (class in immuneML.hyperparameter_optimization.HPSettingResult) HPUtil (class in immuneML.hyperparameter_optimization.core.HPUtil) HTML (immuneML.presentation.PresentationFormat.PresentationFormat attribute) html_templates_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) HTMLBuilder (class in immuneML.presentation.html.HTMLBuilder)

I

id (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) ID_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) identical_overlap() (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) identifier (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) (immuneML.simulation.implants.Motif.Motif attribute) IDENTITY (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IdentitySequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder) ignore_counts (immuneML.util.CompAIRRParams.CompAIRRParams attribute) ignore_genes (immuneML.util.CompAIRRParams.CompAIRRParams attribute) IGoRImport (class in immuneML.IO.dataset_import.IGoRImport) IMGT_CONTINUOUS_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGT_GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGTGappedKmerEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder) IMGTKmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder) immuneML module immuneML.analysis module immuneML.analysis.AxisType module immuneML.analysis.criteria_matches module immuneML.analysis.criteria_matches.BooleanType module immuneML.analysis.criteria_matches.CriteriaMatcher module immuneML.analysis.criteria_matches.CriteriaTypeInstantiator module immuneML.analysis.criteria_matches.DataType module immuneML.analysis.criteria_matches.OperationType module immuneML.analysis.data_manipulation module immuneML.analysis.data_manipulation.DataReshaper module immuneML.analysis.data_manipulation.NormalizationType module immuneML.analysis.data_manipulation.ReductionMethod module immuneML.analysis.entropy_calculations module immuneML.analysis.entropy_calculations.EntropyCalculator module immuneML.analysis.SequenceMatcher module immuneML.analysis.similarities module immuneML.analysis.similarities.SimilarityMeasureType module immuneML.api module immuneML.api.aggregated_runs module immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool module immuneML.api.api_encoding module immuneML.api.galaxy module immuneML.api.galaxy.DatasetGenerationTool module immuneML.api.galaxy.DataSimulationTool module immuneML.api.galaxy.GalaxyMLApplicationTool module immuneML.api.galaxy.GalaxySimulationTool module immuneML.api.galaxy.GalaxyTool module immuneML.api.galaxy.GalaxyTrainMLModel module immuneML.api.galaxy.GalaxyYamlTool module immuneML.api.galaxy.RepertoireClassificationTool module immuneML.api.galaxy.Util module immuneML.app module immuneML.app.ImmuneMLApp module immuneML.caching module immuneML.caching.CacheHandler module immuneML.caching.CacheObjectType module immuneML.caching.CacheType module immuneML.data_model module immuneML.dev_util module immuneML.dev_util.util module immuneML.dsl module immuneML.dsl.DefaultParamsLoader module immuneML.dsl.definition_parsers module immuneML.dsl.definition_parsers.DefinitionParser module immuneML.dsl.definition_parsers.DefinitionParserOutput module immuneML.dsl.definition_parsers.EncodingParser module immuneML.dsl.definition_parsers.MLParser module immuneML.dsl.definition_parsers.MotifParser module immuneML.dsl.definition_parsers.PreprocessingParser module immuneML.dsl.definition_parsers.ReportParser module immuneML.dsl.definition_parsers.SignalParser module immuneML.dsl.definition_parsers.SimulationParser module immuneML.dsl.ImmuneMLParser module immuneML.dsl.import_parsers module immuneML.dsl.import_parsers.ImportParser module immuneML.dsl.instruction_parsers module immuneML.dsl.instruction_parsers.DatasetExportParser module immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser module immuneML.dsl.instruction_parsers.LabelHelper module immuneML.dsl.instruction_parsers.MLApplicationParser module immuneML.dsl.instruction_parsers.SubsamplingParser module immuneML.dsl.instruction_parsers.TrainMLModelParser module immuneML.dsl.InstructionParser module immuneML.dsl.ObjectParser module immuneML.dsl.OutputParser module immuneML.dsl.Parser module immuneML.dsl.semantic_model module immuneML.dsl.semantic_model.MLResult module immuneML.dsl.semantic_model.SemanticModel module immuneML.dsl.symbol_table module immuneML.dsl.symbol_table.SymbolTable module immuneML.dsl.symbol_table.SymbolTableEntry module immuneML.dsl.symbol_table.SymbolType module immuneML.encodings module immuneML.encodings.abundance_encoding module immuneML.encodings.abundance_encoding.AbundanceEncoderHelper module immuneML.encodings.abundance_encoding.CompAIRRBatchIterator module immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder module immuneML.encodings.abundance_encoding.KmerAbundanceEncoder module immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder module immuneML.encodings.atchley_kmer_encoding module immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder module immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType module immuneML.encodings.atchley_kmer_encoding.Util module immuneML.encodings.DatasetEncoder module immuneML.encodings.deeprc module immuneML.encodings.deeprc.DeepRCEncoder module immuneML.encodings.distance_encoding module immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder module immuneML.encodings.distance_encoding.DistanceEncoder module immuneML.encodings.distance_encoding.DistanceMetricType module immuneML.encodings.distance_encoding.TCRdistEncoder module immuneML.encodings.EncoderParams module immuneML.encodings.evenness_profile module immuneML.encodings.evenness_profile.EvennessProfileEncoder module immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder module immuneML.encodings.kmer_frequency module immuneML.encodings.kmer_frequency.KmerFreqReceptorEncoder module immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder module immuneML.encodings.kmer_frequency.KmerFreqSequenceEncoder module immuneML.encodings.kmer_frequency.KmerFrequencyEncoder module immuneML.encodings.kmer_frequency.sequence_encoding module immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder module immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder module immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder module immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder module immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder module immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy module immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType module immuneML.encodings.onehot module immuneML.encodings.onehot.OneHotEncoder module immuneML.encodings.onehot.OneHotReceptorEncoder module immuneML.encodings.onehot.OneHotRepertoireEncoder module immuneML.encodings.onehot.OneHotSequenceEncoder module immuneML.encodings.preprocessing module immuneML.encodings.preprocessing.FeatureScaler module immuneML.encodings.reference_encoding module immuneML.encodings.reference_encoding.MatchedReceptorsEncoder module immuneML.encodings.reference_encoding.MatchedReferenceUtil module immuneML.encodings.reference_encoding.MatchedRegexEncoder module immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder module immuneML.encodings.reference_encoding.MatchedSequencesEncoder module immuneML.encodings.reference_encoding.SequenceMatchingSummaryType module immuneML.encodings.word2vec module immuneML.encodings.word2vec.model_creator module immuneML.encodings.word2vec.model_creator.KmerPairModelCreator module immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy module immuneML.encodings.word2vec.model_creator.ModelType module immuneML.encodings.word2vec.model_creator.SequenceModelCreator module immuneML.encodings.word2vec.W2VRepertoireEncoder module immuneML.encodings.word2vec.W2VSequenceEncoder module immuneML.encodings.word2vec.Word2VecEncoder module immuneML.environment module immuneML.environment.Constants module immuneML.environment.EnvironmentSettings module immuneML.environment.Label module immuneML.environment.LabelConfiguration module immuneML.environment.LabelType module immuneML.environment.SequenceType module immuneML.hyperparameter_optimization module immuneML.hyperparameter_optimization.config module immuneML.hyperparameter_optimization.config.LeaveOneOutConfig module immuneML.hyperparameter_optimization.config.ManualSplitConfig module immuneML.hyperparameter_optimization.config.ReportConfig module immuneML.hyperparameter_optimization.config.SplitConfig module immuneML.hyperparameter_optimization.config.SplitType module immuneML.hyperparameter_optimization.core module immuneML.hyperparameter_optimization.core.HPAssessment module immuneML.hyperparameter_optimization.core.HPSelection module immuneML.hyperparameter_optimization.core.HPUtil module immuneML.hyperparameter_optimization.HPSetting module immuneML.hyperparameter_optimization.HPSettingResult module immuneML.hyperparameter_optimization.states module immuneML.hyperparameter_optimization.states.HPAssessmentState module immuneML.hyperparameter_optimization.states.HPItem module immuneML.hyperparameter_optimization.states.HPLabelState module immuneML.hyperparameter_optimization.states.HPSelectionState module immuneML.hyperparameter_optimization.states.TrainMLModelState module immuneML.hyperparameter_optimization.strategy module immuneML.hyperparameter_optimization.strategy.GridSearch module immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy module immuneML.IO module immuneML.IO.dataset_export module immuneML.IO.dataset_export.AIRRExporter module immuneML.IO.dataset_export.DataExporter module immuneML.IO.dataset_import module immuneML.IO.dataset_import.AIRRImport module immuneML.IO.dataset_import.DataImport module immuneML.IO.dataset_import.DatasetImportParams module immuneML.IO.dataset_import.GenericImport module immuneML.IO.dataset_import.IGoRImport module immuneML.IO.dataset_import.ImmunoSEQRearrangementImport module immuneML.IO.dataset_import.ImmunoSEQSampleImport module immuneML.IO.dataset_import.IReceptorImport module immuneML.IO.dataset_import.MiXCRImport module immuneML.IO.dataset_import.OLGAImport module immuneML.IO.dataset_import.RandomReceptorDatasetImport module immuneML.IO.dataset_import.RandomRepertoireDatasetImport module immuneML.IO.dataset_import.RandomSequenceDatasetImport module immuneML.IO.dataset_import.TenxGenomicsImport module immuneML.IO.dataset_import.VDJdbImport module immuneML.IO.ml_method module immuneML.IO.ml_method.MLExporter module immuneML.IO.ml_method.MLImport module immuneML.IO.ml_method.MLMethodConfiguration module immuneML.IO.ml_method.UtilIO module immuneML.ml_methods module immuneML.ml_methods.classifiers module immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier module immuneML.ml_methods.classifiers.DeepRC module immuneML.ml_methods.classifiers.KNN module immuneML.ml_methods.classifiers.LogisticRegression module immuneML.ml_methods.classifiers.MLMethod module immuneML.ml_methods.classifiers.PrecomputedKNN module immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier module immuneML.ml_methods.classifiers.RandomForestClassifier module immuneML.ml_methods.classifiers.ReceptorCNN module immuneML.ml_methods.classifiers.SklearnMethod module immuneML.ml_methods.classifiers.SVC module immuneML.ml_methods.classifiers.SVM module immuneML.ml_methods.classifiers.TCRdistClassifier module immuneML.ml_methods.generative_models module immuneML.ml_methods.generative_models.BackgroundSequences module immuneML.ml_methods.generative_models.ExperimentalImport module immuneML.ml_methods.generative_models.GenerativeModel module immuneML.ml_methods.generative_models.InternalOlgaModel module immuneML.ml_methods.generative_models.OLGA module

immuneML.ml_methods.generative_models.PWM module immuneML.ml_methods.generative_models.SimpleLSTM module immuneML.ml_methods.generative_models.SimpleVAE module immuneML.ml_methods.generative_models.SoNNia module immuneML.ml_methods.pytorch_implementations module immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module immuneML.ml_methods.util module immuneML.ml_methods.util.Util module immuneML.ml_metrics module immuneML.ml_metrics.MetricUtil module immuneML.ml_metrics.ml_metrics module immuneML.pairwise_repertoire_comparison module immuneML.pairwise_repertoire_comparison.ComparisonData module immuneML.pairwise_repertoire_comparison.ComparisonDataBatch module immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison module immuneML.preprocessing module immuneML.preprocessing.filters module immuneML.preprocessing.filters.ChainRepertoireFilter module immuneML.preprocessing.filters.ClonesPerRepertoireFilter module immuneML.preprocessing.filters.CountAggregationFunction module immuneML.preprocessing.filters.CountPerSequenceFilter module immuneML.preprocessing.filters.DuplicateSequenceFilter module immuneML.preprocessing.filters.Filter module immuneML.preprocessing.filters.MetadataRepertoireFilter module immuneML.preprocessing.filters.SequenceLengthFilter module immuneML.preprocessing.Preprocessor module immuneML.preprocessing.ReferenceSequenceAnnotator module immuneML.preprocessing.SubjectRepertoireCollector module immuneML.presentation module immuneML.presentation.html module immuneML.presentation.html.DatasetExportHTMLBuilder module immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder module immuneML.presentation.html.HPHTMLBuilder module immuneML.presentation.html.HTMLBuilder module immuneML.presentation.html.MLApplicationHTMLBuilder module immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder module immuneML.presentation.html.SubsamplingHTMLBuilder module immuneML.presentation.html.Util module immuneML.presentation.InstructionPresentation module immuneML.presentation.PresentationFactory module immuneML.presentation.PresentationFormat module immuneML.presentation.TemplateParser module immuneML.reports module immuneML.reports.data_reports module immuneML.reports.data_reports.AminoAcidFrequencyDistribution module immuneML.reports.data_reports.DataReport module immuneML.reports.data_reports.GLIPH2Exporter module immuneML.reports.data_reports.ReceptorDatasetOverview module immuneML.reports.data_reports.RecoveredSignificantFeatures module immuneML.reports.data_reports.RepertoireClonotypeSummary module immuneML.reports.data_reports.SequenceLengthDistribution module immuneML.reports.data_reports.SequencesWithSignificantKmers module immuneML.reports.data_reports.SignificantFeatures module immuneML.reports.data_reports.SignificantKmerPositions module immuneML.reports.data_reports.SimpleDatasetOverview module immuneML.reports.encoding_reports module immuneML.reports.encoding_reports.DesignMatrixExporter module immuneML.reports.encoding_reports.EncodingReport module immuneML.reports.encoding_reports.FeatureComparison module immuneML.reports.encoding_reports.FeatureDistribution module immuneML.reports.encoding_reports.FeatureReport module immuneML.reports.encoding_reports.FeatureValueBarplot module immuneML.reports.encoding_reports.Matches module immuneML.reports.encoding_reports.RelevantSequenceExporter module immuneML.reports.gen_model_reports module immuneML.reports.gen_model_reports.GenModelReport module immuneML.reports.gen_model_reports.VAESummary module immuneML.reports.ml_reports module immuneML.reports.ml_reports.CoefficientPlottingSetting module immuneML.reports.ml_reports.CoefficientPlottingSettingList module immuneML.reports.ml_reports.Coefficients module immuneML.reports.ml_reports.ConfounderAnalysis module immuneML.reports.ml_reports.DeepRCMotifDiscovery module immuneML.reports.ml_reports.KernelSequenceLogo module immuneML.reports.ml_reports.MLReport module immuneML.reports.ml_reports.MotifSeedRecovery module immuneML.reports.ml_reports.ROCCurve module immuneML.reports.ml_reports.SequenceAssociationLikelihood module immuneML.reports.ml_reports.TCRdistMotifDiscovery module immuneML.reports.ml_reports.TrainingPerformance module immuneML.reports.multi_dataset_reports module immuneML.reports.multi_dataset_reports.DiseaseAssociatedSequenceOverlap module immuneML.reports.multi_dataset_reports.MultiDatasetReport module immuneML.reports.multi_dataset_reports.PerformanceOverview module immuneML.reports.PlotlyUtil module immuneML.reports.Report module immuneML.reports.ReportOutput module immuneML.reports.ReportResult module immuneML.reports.ReportUtil module immuneML.reports.train_ml_model_reports module immuneML.reports.train_ml_model_reports.CVFeaturePerformance module immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap module immuneML.reports.train_ml_model_reports.MLSettingsPerformance module immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap module immuneML.reports.train_ml_model_reports.ROCCurveSummary module immuneML.reports.train_ml_model_reports.TrainMLModelReport module immuneML.simulation module immuneML.simulation.dataset_generation module immuneML.simulation.dataset_generation.RandomDatasetGenerator module immuneML.simulation.implants module immuneML.simulation.implants.ImplantAnnotation module immuneML.simulation.implants.Motif module immuneML.simulation.implants.MotifInstance module immuneML.simulation.implants.Signal module immuneML.simulation.motif_instantiation_strategy module immuneML.simulation.sequence_implanting module immuneML.simulation.signal_implanting module immuneML.simulation.signal_implanting_strategy module immuneML.simulation.simulation_strategy module immuneML.simulation.simulation_strategy.ImplantingStrategy module immuneML.simulation.simulation_strategy.RejectionSamplingStrategy module immuneML.simulation.simulation_strategy.SimulationStrategy module immuneML.simulation.util module immuneML.simulation.util.bnp_util module immuneML.simulation.util.igor_helper module immuneML.simulation.util.util module immuneML.util module immuneML.util.AdaptiveImportHelper module immuneML.util.CompAIRRHelper module immuneML.util.CompAIRRParams module immuneML.util.DistanceMetrics module immuneML.util.DocEnumHelper module immuneML.util.EncoderHelper module immuneML.util.FilenameHandler module immuneML.util.ImportHelper module immuneML.util.KmerHelper module immuneML.util.Logger module immuneML.util.NameBuilder module immuneML.util.NumpyHelper module immuneML.util.ParameterValidator module immuneML.util.PathBuilder module immuneML.util.PositionHelper module immuneML.util.ReadsType module immuneML.util.ReflectionHandler module immuneML.util.RepertoireBuilder module immuneML.util.SequenceAnalysisHelper module immuneML.util.SignificantFeaturesHelper module immuneML.util.StringHelper module immuneML.util.TCRdistHelper module immuneML.workflows module immuneML.workflows.instructions module immuneML.workflows.instructions.dataset_generation module immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction module immuneML.workflows.instructions.dataset_generation.DatasetExportState module immuneML.workflows.instructions.exploratory_analysis module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit module immuneML.workflows.instructions.Instruction module immuneML.workflows.instructions.ligo_sim_feasibility module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports module immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction module immuneML.workflows.instructions.ligo_simulation module immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction module immuneML.workflows.instructions.ml_model_application module immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction module immuneML.workflows.instructions.ml_model_application.MLApplicationState module immuneML.workflows.instructions.MLProcess module immuneML.workflows.instructions.quickstart module immuneML.workflows.instructions.subsampling module immuneML.workflows.instructions.subsampling.SubsamplingInstruction module immuneML.workflows.instructions.subsampling.SubsamplingState module immuneML.workflows.instructions.train_gen_model module immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction module immuneML.workflows.instructions.TrainMLModelInstruction module immuneML.workflows.steps module immuneML.workflows.steps.data_splitter module immuneML.workflows.steps.data_splitter.DataSplitter module immuneML.workflows.steps.data_splitter.DataSplitterParams module immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter module immuneML.workflows.steps.data_splitter.ManualSplitter module immuneML.workflows.steps.data_splitter.Util module immuneML.workflows.steps.DataEncoder module immuneML.workflows.steps.DataEncoderParams module immuneML.workflows.steps.MLMethodAssessment module immuneML.workflows.steps.MLMethodAssessmentParams module immuneML.workflows.steps.MLMethodTrainer module immuneML.workflows.steps.MLMethodTrainerParams module immuneML.workflows.steps.Step module immuneML.workflows.steps.StepParams module ImmuneMLApp (class in immuneML.app.ImmuneMLApp) ImmuneMLParser (class in immuneML.dsl.ImmuneMLParser) ImmunoSEQRearrangementImport (class in immuneML.IO.dataset_import.ImmunoSEQRearrangementImport) ImmunoSEQSampleImport (class in immuneML.IO.dataset_import.ImmunoSEQSampleImport) ImplantAnnotation (class in immuneML.simulation.implants.ImplantAnnotation) ImplantingStrategy (class in immuneML.simulation.simulation_strategy.ImplantingStrategy) import_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) import_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.RandomReceptorDatasetImport.RandomReceptorDatasetImport method) (immuneML.IO.dataset_import.RandomRepertoireDatasetImport.RandomRepertoireDatasetImport method) (immuneML.IO.dataset_import.RandomSequenceDatasetImport.RandomSequenceDatasetImport method) import_dataset_from_yaml() (immuneML.IO.dataset_import.DataImport.DataImport method) import_element_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) import_empty_aa_sequences (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_empty_nt_sequences (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_encoder() (immuneML.IO.ml_method.MLImport.MLImport static method) import_function() (immuneML.util.ReflectionHandler.ReflectionHandler static method) import_hp_setting() (immuneML.IO.ml_method.MLImport.MLImport static method) import_illegal_characters (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_label() (immuneML.IO.ml_method.MLImport.MLImport static method) import_module() (immuneML.util.ReflectionHandler.ReflectionHandler static method) import_out_of_frame (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_pairwise_comparison() (immuneML.IO.ml_method.UtilIO.UtilIO static method) import_preprocessing_sequence() (immuneML.IO.ml_method.MLImport.MLImport static method) import_productive (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_receptor_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) import_repertoire_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport method) import_sequence_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport method) import_unknown_productivity (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_unproductive (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_with_stop_codon (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) ImportHelper (class in immuneML.util.ImportHelper) ImportParser (class in immuneML.dsl.import_parsers.ImportParser) IN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) indels (immuneML.util.CompAIRRParams.CompAIRRParams attribute) info (immuneML.reports.ReportResult.ReportResult attribute) INPUT_FILENAME (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) insert() (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) instantiate() (immuneML.analysis.criteria_matches.CriteriaTypeInstantiator.CriteriaTypeInstantiator static method) instantiate_motif() (immuneML.simulation.implants.Motif.Motif method) Instruction (class in immuneML.workflows.instructions.Instruction) INSTRUCTION (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) instruction_class (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) instruction_name (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) InstructionParser (class in immuneML.dsl.InstructionParser) InstructionPresentation (class in immuneML.presentation.InstructionPresentation) InternalOlgaModel (class in immuneML.ml_methods.generative_models.InternalOlgaModel) INVALID_COLNAME_CHARS (immuneML.util.ImportHelper.ImportHelper attribute) INVALID_P_VALUE (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper attribute) IReceptorImport (class in immuneML.IO.dataset_import.IReceptorImport) is_cdr3 (immuneML.util.CompAIRRParams.CompAIRRParams attribute) is_illegal_sequence() (immuneML.util.ImportHelper.ImportHelper static method) is_installed() (immuneML.util.ReflectionHandler.ReflectionHandler static method) is_nan_or_empty() (immuneML.util.NumpyHelper.NumpyHelper static method) is_present_custom_func (immuneML.simulation.implants.Signal.Signal attribute) is_repertoire (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) is_same() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) is_simple_type() (immuneML.util.NumpyHelper.NumpyHelper static method) is_valid_sequence_str() (in module immuneML.util.AdaptiveImportHelper) is_vdj (immuneML.ml_methods.generative_models.OLGA.OLGA property) items (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) ITER_TO_REPORT (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM attribute)

J

j_call (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) j_gene_mapping (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute)

JACCARD (immuneML.analysis.similarities.SimilarityMeasureType.SimilarityMeasureType attribute) (immuneML.encodings.distance_encoding.DistanceMetricType.DistanceMetricType attribute) jaccard() (in module immuneML.util.DistanceMetrics)

K

K_FOLD (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) k_fold_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) keep_compairr_input (immuneML.util.CompAIRRParams.CompAIRRParams attribute) keeps_example_count() (immuneML.preprocessing.filters.ChainRepertoireFilter.ChainRepertoireFilter method) (immuneML.preprocessing.filters.ClonesPerRepertoireFilter.ClonesPerRepertoireFilter method) (immuneML.preprocessing.filters.CountPerSequenceFilter.CountPerSequenceFilter method) (immuneML.preprocessing.filters.MetadataRepertoireFilter.MetadataRepertoireFilter method) (immuneML.preprocessing.Preprocessor.Preprocessor method) (immuneML.preprocessing.SubjectRepertoireCollector.SubjectRepertoireCollector method) KernelSequenceLogo (class in immuneML.reports.ml_reports.KernelSequenceLogo) KEY_MAPPING (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport attribute) keyword (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser attribute) (immuneML.dsl.definition_parsers.MLParser.MLParser attribute) (immuneML.dsl.definition_parsers.MotifParser.MotifParser attribute) (immuneML.dsl.definition_parsers.PreprocessingParser.PreprocessingParser attribute) (immuneML.dsl.definition_parsers.ReportParser.ReportParser attribute) (immuneML.dsl.definition_parsers.SignalParser.SignalParser attribute) (immuneML.dsl.definition_parsers.SimulationParser.SimulationParser attribute) (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute) (immuneML.dsl.InstructionParser.InstructionParser attribute)

KMER_PAIR (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) KmerAbundanceEncoder (class in immuneML.encodings.abundance_encoding.KmerAbundanceEncoder) KmerFreqReceptorEncoder (class in immuneML.encodings.kmer_frequency.KmerFreqReceptorEncoder) KmerFreqRepertoireEncoder (class in immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder) KmerFreqSequenceEncoder (class in immuneML.encodings.kmer_frequency.KmerFreqSequenceEncoder) KmerFrequencyEncoder (class in immuneML.encodings.kmer_frequency.KmerFrequencyEncoder) KmerHelper (class in immuneML.util.KmerHelper) KmerPairModelCreator (class in immuneML.encodings.word2vec.model_creator.KmerPairModelCreator) KmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder) KNN (class in immuneML.ml_methods.classifiers.KNN)

L

L2 (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) Label (class in immuneML.environment.Label) label_columns (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) label_config (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) label_configuration (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) label_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) label_positive_class (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) label_values (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) LabelConfiguration (class in immuneML.environment.LabelConfiguration) LabelHelper (class in immuneML.dsl.instruction_parsers.LabelHelper) LabelType (class in immuneML.environment.LabelType) LAST (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) learn_model (immuneML.encodings.EncoderParams.EncoderParams attribute) LEAVE_ONE_OUT_STRATIFICATION (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) leave_one_out_stratification_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) LeaveOneOutConfig (class in immuneML.hyperparameter_optimization.config.LeaveOneOutConfig) LeaveOneOutSplitter (class in immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter) LESS_THAN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) LigoSimInstruction (class in immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction) load() (immuneML.dsl.DefaultParamsLoader.DefaultParamsLoader static method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) load_alleles() (in module immuneML.IO.dataset_import.MiXCRImport)

load_attribute() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) load_encoded_data() (in module immuneML.dev_util.util) load_encoder() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder static method) (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder static method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder static method) load_file() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport method) load_internal_model() (immuneML.ml_methods.generative_models.OLGA.OLGA method) load_model() (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel class method) (immuneML.ml_methods.generative_models.OLGA.OLGA class method) (immuneML.ml_methods.generative_models.PWM.PWM class method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM class method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE class method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia class method) load_repertoire_object() (immuneML.IO.dataset_import.DataImport.DataImport method) load_sequence_dataframe() (immuneML.IO.dataset_import.DataImport.DataImport method) load_sequences() (immuneML.util.SignificantFeaturesHelper.SignificantFeaturesHelper static method) load_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) locus (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) log() (in module immuneML.util.Logger) log_dataset_info() (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) LOG_FILENAME (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) log_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) LogisticRegression (class in immuneML.ml_methods.classifiers.LogisticRegression) LOOCV (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) loocv_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) low_memory (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute)

M

main() (in module immuneML.app.ImmuneMLApp) (in module immuneML.workflows.instructions.quickstart) make_annotated_dataclass() (in module immuneML.simulation.util.util) make_binary_class_mapping() (immuneML.ml_methods.util.Util.Util static method) make_bnp_annotated_sequences() (in module immuneML.simulation.util.util) make_class_mapping() (immuneML.ml_methods.util.Util.Util static method) make_data_loader() (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) make_dataset() (immuneML.workflows.steps.data_splitter.Util.Util static method) make_dataset_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_dataset_html_map() (immuneML.presentation.html.Util.Util static method) make_docs() (immuneML.dsl.InstructionParser.InstructionParser static method) make_downloadable_zip() (immuneML.presentation.html.Util.Util static method) make_encodings_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_fisher_function() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) make_gene_call_from_gene_and_allele() (in module immuneML.util.AdaptiveImportHelper) make_html_map() (immuneML.presentation.html.DatasetExportHTMLBuilder.DatasetExportHTMLBuilder static method) (immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder.ExploratoryAnalysisHTMLBuilder static method) (immuneML.presentation.html.MLApplicationHTMLBuilder.MLApplicationHTMLBuilder static method) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder static method) make_ml_methods_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_motif_instances() (immuneML.simulation.implants.Signal.Signal method) make_new_metadata_file() (immuneML.util.ImportHelper.ImportHelper static method) make_new_model() (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) make_preprocessing_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_presentation_builder() (immuneML.presentation.PresentationFactory.PresentationFactory static method) make_repertoire_from_sequences() (in module immuneML.simulation.util.util) make_report_builder() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) make_reports_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_sequence_paths() (in module immuneML.simulation.util.util) make_signal_metadata() (in module immuneML.simulation.util.util) make_simulation_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_skewed_model_files() (in module immuneML.simulation.util.igor_helper) MANUAL (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) manual_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) ManualSplitConfig (class in immuneML.hyperparameter_optimization.config.ManualSplitConfig) ManualSplitter (class in immuneML.workflows.steps.data_splitter.ManualSplitter) map_to_new_class_values() (immuneML.ml_methods.util.Util.Util static method) map_to_old_class_values() (immuneML.ml_methods.util.Util.Util static method) match() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher method) (immuneML.analysis.SequenceMatcher.SequenceMatcher method) match_genes() (in module immuneML.simulation.util.util) match_motif() (in module immuneML.simulation.util.util) match_motif_group() (in module immuneML.simulation.util.util) match_motif_regexes() (in module immuneML.simulation.util.util) match_repertoire() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) match_sequence() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) MatchedReceptorsEncoder (class in immuneML.encodings.reference_encoding.MatchedReceptorsEncoder) MatchedReferenceUtil (class in immuneML.encodings.reference_encoding.MatchedReferenceUtil) MatchedRegexEncoder (class in immuneML.encodings.reference_encoding.MatchedRegexEncoder) MatchedRegexRepertoireEncoder (class in immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder) MatchedSequencesEncoder (class in immuneML.encodings.reference_encoding.MatchedSequencesEncoder) Matches (class in immuneML.reports.encoding_reports.Matches) matches_gene() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) matches_sequence() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) matrix (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) MAX (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) MAX_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) MAX_ELEMENT_COUNT_TO_SHOW (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelInstruction attribute) MAX_MOTIFS_PER_SEQUENCE (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy attribute) max_overlap_sliding() (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) MAX_SEED_VALUE (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier attribute) max_sequence_length (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) MAX_SIG_FREQ (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction attribute) MAX_SIGNALS_PER_SEQUENCE (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy attribute) MEAN (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) memo() (immuneML.caching.CacheHandler.CacheHandler static method) memo_by_params() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) merge_dataclass_objects() (in module immuneML.simulation.util.bnp_util) merge_tmp_batches_to_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) METADATA_EXTENSION (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) metadata_file (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) METADATA_SEP (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) MetadataRepertoireFilter (class in immuneML.preprocessing.filters.MetadataRepertoireFilter) method (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) metrics (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) metrics_path (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) MetricUtil (class in immuneML.ml_metrics.MetricUtil) MIDPOINT_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) MIN (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) MIN_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) min_count (immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig attribute) min_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) MIN_RANGE_PROBABILITY (immuneML.simulation.simulation_strategy.ImplantingStrategy.ImplantingStrategy attribute) (immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction.LigoSimInstruction attribute) MIN_SEED_VALUE (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier attribute) MIN_SIG_FREQ (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction attribute) MiXCRImport (class in immuneML.IO.dataset_import.MiXCRImport) ML_METHOD (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) ml_method (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) ml_method_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) ml_settings_export_path (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) MLApplicationHTMLBuilder (class in immuneML.presentation.html.MLApplicationHTMLBuilder) MLApplicationInstruction (class in immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction) MLApplicationParser (class in immuneML.dsl.instruction_parsers.MLApplicationParser) MLApplicationState (class in immuneML.workflows.instructions.ml_model_application.MLApplicationState) MLExporter (class in immuneML.IO.ml_method.MLExporter) MLImport (class in immuneML.IO.ml_method.MLImport) MLMethod (class in immuneML.ml_methods.classifiers.MLMethod) MLMethodAssessment (class in immuneML.workflows.steps.MLMethodAssessment) MLMethodAssessmentParams (class in immuneML.workflows.steps.MLMethodAssessmentParams) MLMethodConfiguration (class in immuneML.IO.ml_method.MLMethodConfiguration) MLMethodTrainer (class in immuneML.workflows.steps.MLMethodTrainer) MLMethodTrainerParams (class in immuneML.workflows.steps.MLMethodTrainerParams) MLParser (class in immuneML.dsl.definition_parsers.MLParser) MLProcess (class in immuneML.workflows.instructions.MLProcess) MLReport (class in immuneML.reports.ml_reports.MLReport) MLResult (class in immuneML.dsl.semantic_model.MLResult) MLSettingsPerformance (class in immuneML.reports.train_ml_model_reports.MLSettingsPerformance) model (immuneML.encodings.EncoderParams.EncoderParams attribute) MODEL_FILENAMES (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) model_path (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) model_report_results (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) ModelCreatorStrategy (class in immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy) ModelType (class in immuneML.encodings.word2vec.model_creator.ModelType) module immuneML immuneML.analysis immuneML.analysis.AxisType immuneML.analysis.criteria_matches immuneML.analysis.criteria_matches.BooleanType immuneML.analysis.criteria_matches.CriteriaMatcher immuneML.analysis.criteria_matches.CriteriaTypeInstantiator immuneML.analysis.criteria_matches.DataType immuneML.analysis.criteria_matches.OperationType immuneML.analysis.data_manipulation immuneML.analysis.data_manipulation.DataReshaper immuneML.analysis.data_manipulation.NormalizationType immuneML.analysis.data_manipulation.ReductionMethod immuneML.analysis.entropy_calculations immuneML.analysis.entropy_calculations.EntropyCalculator immuneML.analysis.SequenceMatcher immuneML.analysis.similarities immuneML.analysis.similarities.SimilarityMeasureType immuneML.api immuneML.api.aggregated_runs immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool immuneML.api.api_encoding immuneML.api.galaxy immuneML.api.galaxy.DatasetGenerationTool immuneML.api.galaxy.DataSimulationTool immuneML.api.galaxy.GalaxyMLApplicationTool immuneML.api.galaxy.GalaxySimulationTool immuneML.api.galaxy.GalaxyTool immuneML.api.galaxy.GalaxyTrainMLModel immuneML.api.galaxy.GalaxyYamlTool immuneML.api.galaxy.RepertoireClassificationTool immuneML.api.galaxy.Util immuneML.app immuneML.app.ImmuneMLApp immuneML.caching immuneML.caching.CacheHandler immuneML.caching.CacheObjectType immuneML.caching.CacheType immuneML.data_model immuneML.dev_util immuneML.dev_util.util immuneML.dsl immuneML.dsl.DefaultParamsLoader immuneML.dsl.definition_parsers immuneML.dsl.definition_parsers.DefinitionParser immuneML.dsl.definition_parsers.DefinitionParserOutput immuneML.dsl.definition_parsers.EncodingParser immuneML.dsl.definition_parsers.MLParser immuneML.dsl.definition_parsers.MotifParser immuneML.dsl.definition_parsers.PreprocessingParser immuneML.dsl.definition_parsers.ReportParser immuneML.dsl.definition_parsers.SignalParser immuneML.dsl.definition_parsers.SimulationParser immuneML.dsl.ImmuneMLParser immuneML.dsl.import_parsers immuneML.dsl.import_parsers.ImportParser immuneML.dsl.instruction_parsers immuneML.dsl.instruction_parsers.DatasetExportParser immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser immuneML.dsl.instruction_parsers.LabelHelper immuneML.dsl.instruction_parsers.MLApplicationParser immuneML.dsl.instruction_parsers.SubsamplingParser immuneML.dsl.instruction_parsers.TrainMLModelParser immuneML.dsl.InstructionParser immuneML.dsl.ObjectParser immuneML.dsl.OutputParser immuneML.dsl.Parser immuneML.dsl.semantic_model immuneML.dsl.semantic_model.MLResult immuneML.dsl.semantic_model.SemanticModel immuneML.dsl.symbol_table immuneML.dsl.symbol_table.SymbolTable immuneML.dsl.symbol_table.SymbolTableEntry immuneML.dsl.symbol_table.SymbolType immuneML.encodings immuneML.encodings.abundance_encoding immuneML.encodings.abundance_encoding.AbundanceEncoderHelper immuneML.encodings.abundance_encoding.CompAIRRBatchIterator immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder immuneML.encodings.abundance_encoding.KmerAbundanceEncoder immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder immuneML.encodings.atchley_kmer_encoding immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType immuneML.encodings.atchley_kmer_encoding.Util immuneML.encodings.DatasetEncoder immuneML.encodings.deeprc immuneML.encodings.deeprc.DeepRCEncoder immuneML.encodings.distance_encoding immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder immuneML.encodings.distance_encoding.DistanceEncoder immuneML.encodings.distance_encoding.DistanceMetricType immuneML.encodings.distance_encoding.TCRdistEncoder immuneML.encodings.EncoderParams immuneML.encodings.evenness_profile immuneML.encodings.evenness_profile.EvennessProfileEncoder immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder immuneML.encodings.kmer_frequency immuneML.encodings.kmer_frequency.KmerFreqReceptorEncoder immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder immuneML.encodings.kmer_frequency.KmerFreqSequenceEncoder immuneML.encodings.kmer_frequency.KmerFrequencyEncoder immuneML.encodings.kmer_frequency.sequence_encoding immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType immuneML.encodings.onehot immuneML.encodings.onehot.OneHotEncoder immuneML.encodings.onehot.OneHotReceptorEncoder immuneML.encodings.onehot.OneHotRepertoireEncoder immuneML.encodings.onehot.OneHotSequenceEncoder immuneML.encodings.preprocessing immuneML.encodings.preprocessing.FeatureScaler immuneML.encodings.reference_encoding immuneML.encodings.reference_encoding.MatchedReceptorsEncoder immuneML.encodings.reference_encoding.MatchedReferenceUtil immuneML.encodings.reference_encoding.MatchedRegexEncoder immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder immuneML.encodings.reference_encoding.MatchedSequencesEncoder immuneML.encodings.reference_encoding.SequenceMatchingSummaryType immuneML.encodings.word2vec immuneML.encodings.word2vec.model_creator immuneML.encodings.word2vec.model_creator.KmerPairModelCreator immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy immuneML.encodings.word2vec.model_creator.ModelType immuneML.encodings.word2vec.model_creator.SequenceModelCreator immuneML.encodings.word2vec.W2VRepertoireEncoder immuneML.encodings.word2vec.W2VSequenceEncoder immuneML.encodings.word2vec.Word2VecEncoder immuneML.environment immuneML.environment.Constants immuneML.environment.EnvironmentSettings immuneML.environment.Label immuneML.environment.LabelConfiguration immuneML.environment.LabelType immuneML.environment.SequenceType immuneML.hyperparameter_optimization immuneML.hyperparameter_optimization.config immuneML.hyperparameter_optimization.config.LeaveOneOutConfig immuneML.hyperparameter_optimization.config.ManualSplitConfig immuneML.hyperparameter_optimization.config.ReportConfig immuneML.hyperparameter_optimization.config.SplitConfig immuneML.hyperparameter_optimization.config.SplitType immuneML.hyperparameter_optimization.core immuneML.hyperparameter_optimization.core.HPAssessment immuneML.hyperparameter_optimization.core.HPSelection immuneML.hyperparameter_optimization.core.HPUtil immuneML.hyperparameter_optimization.HPSetting immuneML.hyperparameter_optimization.HPSettingResult immuneML.hyperparameter_optimization.states immuneML.hyperparameter_optimization.states.HPAssessmentState immuneML.hyperparameter_optimization.states.HPItem immuneML.hyperparameter_optimization.states.HPLabelState immuneML.hyperparameter_optimization.states.HPSelectionState immuneML.hyperparameter_optimization.states.TrainMLModelState immuneML.hyperparameter_optimization.strategy immuneML.hyperparameter_optimization.strategy.GridSearch immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy immuneML.IO immuneML.IO.dataset_export immuneML.IO.dataset_export.AIRRExporter immuneML.IO.dataset_export.DataExporter immuneML.IO.dataset_import immuneML.IO.dataset_import.AIRRImport immuneML.IO.dataset_import.DataImport immuneML.IO.dataset_import.DatasetImportParams immuneML.IO.dataset_import.GenericImport immuneML.IO.dataset_import.IGoRImport immuneML.IO.dataset_import.ImmunoSEQRearrangementImport immuneML.IO.dataset_import.ImmunoSEQSampleImport immuneML.IO.dataset_import.IReceptorImport immuneML.IO.dataset_import.MiXCRImport immuneML.IO.dataset_import.OLGAImport immuneML.IO.dataset_import.RandomReceptorDatasetImport immuneML.IO.dataset_import.RandomRepertoireDatasetImport immuneML.IO.dataset_import.RandomSequenceDatasetImport immuneML.IO.dataset_import.TenxGenomicsImport immuneML.IO.dataset_import.VDJdbImport immuneML.IO.ml_method immuneML.IO.ml_method.MLExporter immuneML.IO.ml_method.MLImport immuneML.IO.ml_method.MLMethodConfiguration immuneML.IO.ml_method.UtilIO immuneML.ml_methods immuneML.ml_methods.classifiers immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier immuneML.ml_methods.classifiers.DeepRC immuneML.ml_methods.classifiers.KNN immuneML.ml_methods.classifiers.LogisticRegression immuneML.ml_methods.classifiers.MLMethod immuneML.ml_methods.classifiers.PrecomputedKNN immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier immuneML.ml_methods.classifiers.RandomForestClassifier immuneML.ml_methods.classifiers.ReceptorCNN immuneML.ml_methods.classifiers.SklearnMethod immuneML.ml_methods.classifiers.SVC immuneML.ml_methods.classifiers.SVM immuneML.ml_methods.classifiers.TCRdistClassifier immuneML.ml_methods.generative_models immuneML.ml_methods.generative_models.BackgroundSequences immuneML.ml_methods.generative_models.ExperimentalImport immuneML.ml_methods.generative_models.GenerativeModel immuneML.ml_methods.generative_models.InternalOlgaModel immuneML.ml_methods.generative_models.OLGA immuneML.ml_methods.generative_models.PWM immuneML.ml_methods.generative_models.SimpleLSTM immuneML.ml_methods.generative_models.SimpleVAE immuneML.ml_methods.generative_models.SoNNia immuneML.ml_methods.pytorch_implementations immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN immuneML.ml_methods.util immuneML.ml_methods.util.Util immuneML.ml_metrics immuneML.ml_metrics.MetricUtil immuneML.ml_metrics.ml_metrics immuneML.pairwise_repertoire_comparison immuneML.pairwise_repertoire_comparison.ComparisonData immuneML.pairwise_repertoire_comparison.ComparisonDataBatch immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison immuneML.preprocessing immuneML.preprocessing.filters immuneML.preprocessing.filters.ChainRepertoireFilter immuneML.preprocessing.filters.ClonesPerRepertoireFilter immuneML.preprocessing.filters.CountAggregationFunction immuneML.preprocessing.filters.CountPerSequenceFilter immuneML.preprocessing.filters.DuplicateSequenceFilter immuneML.preprocessing.filters.Filter immuneML.preprocessing.filters.MetadataRepertoireFilter immuneML.preprocessing.filters.SequenceLengthFilter immuneML.preprocessing.Preprocessor immuneML.preprocessing.ReferenceSequenceAnnotator immuneML.preprocessing.SubjectRepertoireCollector immuneML.presentation immuneML.presentation.html immuneML.presentation.html.DatasetExportHTMLBuilder immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder immuneML.presentation.html.HPHTMLBuilder immuneML.presentation.html.HTMLBuilder immuneML.presentation.html.MLApplicationHTMLBuilder immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder immuneML.presentation.html.SubsamplingHTMLBuilder immuneML.presentation.html.Util immuneML.presentation.InstructionPresentation immuneML.presentation.PresentationFactory immuneML.presentation.PresentationFormat immuneML.presentation.TemplateParser immuneML.reports immuneML.reports.data_reports immuneML.reports.data_reports.AminoAcidFrequencyDistribution immuneML.reports.data_reports.DataReport immuneML.reports.data_reports.GLIPH2Exporter immuneML.reports.data_reports.ReceptorDatasetOverview immuneML.reports.data_reports.RecoveredSignificantFeatures immuneML.reports.data_reports.RepertoireClonotypeSummary immuneML.reports.data_reports.SequenceLengthDistribution immuneML.reports.data_reports.SequencesWithSignificantKmers immuneML.reports.data_reports.SignificantFeatures immuneML.reports.data_reports.SignificantKmerPositions immuneML.reports.data_reports.SimpleDatasetOverview immuneML.reports.encoding_reports immuneML.reports.encoding_reports.DesignMatrixExporter immuneML.reports.encoding_reports.EncodingReport immuneML.reports.encoding_reports.FeatureComparison immuneML.reports.encoding_reports.FeatureDistribution immuneML.reports.encoding_reports.FeatureReport immuneML.reports.encoding_reports.FeatureValueBarplot immuneML.reports.encoding_reports.Matches immuneML.reports.encoding_reports.RelevantSequenceExporter immuneML.reports.gen_model_reports immuneML.reports.gen_model_reports.GenModelReport immuneML.reports.gen_model_reports.VAESummary immuneML.reports.ml_reports immuneML.reports.ml_reports.CoefficientPlottingSetting immuneML.reports.ml_reports.CoefficientPlottingSettingList immuneML.reports.ml_reports.Coefficients immuneML.reports.ml_reports.ConfounderAnalysis immuneML.reports.ml_reports.DeepRCMotifDiscovery immuneML.reports.ml_reports.KernelSequenceLogo immuneML.reports.ml_reports.MLReport immuneML.reports.ml_reports.MotifSeedRecovery immuneML.reports.ml_reports.ROCCurve immuneML.reports.ml_reports.SequenceAssociationLikelihood immuneML.reports.ml_reports.TCRdistMotifDiscovery immuneML.reports.ml_reports.TrainingPerformance immuneML.reports.multi_dataset_reports immuneML.reports.multi_dataset_reports.DiseaseAssociatedSequenceOverlap immuneML.reports.multi_dataset_reports.MultiDatasetReport immuneML.reports.multi_dataset_reports.PerformanceOverview immuneML.reports.PlotlyUtil immuneML.reports.Report immuneML.reports.ReportOutput immuneML.reports.ReportResult immuneML.reports.ReportUtil immuneML.reports.train_ml_model_reports immuneML.reports.train_ml_model_reports.CVFeaturePerformance immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap immuneML.reports.train_ml_model_reports.MLSettingsPerformance immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap immuneML.reports.train_ml_model_reports.ROCCurveSummary immuneML.reports.train_ml_model_reports.TrainMLModelReport immuneML.simulation immuneML.simulation.dataset_generation immuneML.simulation.dataset_generation.RandomDatasetGenerator immuneML.simulation.implants immuneML.simulation.implants.ImplantAnnotation immuneML.simulation.implants.Motif immuneML.simulation.implants.MotifInstance immuneML.simulation.implants.Signal immuneML.simulation.motif_instantiation_strategy immuneML.simulation.sequence_implanting immuneML.simulation.signal_implanting immuneML.simulation.signal_implanting_strategy immuneML.simulation.simulation_strategy immuneML.simulation.simulation_strategy.ImplantingStrategy immuneML.simulation.simulation_strategy.RejectionSamplingStrategy immuneML.simulation.simulation_strategy.SimulationStrategy immuneML.simulation.util immuneML.simulation.util.bnp_util immuneML.simulation.util.igor_helper immuneML.simulation.util.util immuneML.util immuneML.util.AdaptiveImportHelper immuneML.util.CompAIRRHelper immuneML.util.CompAIRRParams immuneML.util.DistanceMetrics immuneML.util.DocEnumHelper immuneML.util.EncoderHelper immuneML.util.FilenameHandler immuneML.util.ImportHelper immuneML.util.KmerHelper immuneML.util.Logger immuneML.util.NameBuilder immuneML.util.NumpyHelper immuneML.util.ParameterValidator immuneML.util.PathBuilder immuneML.util.PositionHelper immuneML.util.ReadsType immuneML.util.ReflectionHandler immuneML.util.RepertoireBuilder immuneML.util.SequenceAnalysisHelper immuneML.util.SignificantFeaturesHelper immuneML.util.StringHelper immuneML.util.TCRdistHelper immuneML.workflows immuneML.workflows.instructions immuneML.workflows.instructions.dataset_generation immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction immuneML.workflows.instructions.dataset_generation.DatasetExportState immuneML.workflows.instructions.exploratory_analysis immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit immuneML.workflows.instructions.Instruction immuneML.workflows.instructions.ligo_sim_feasibility immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction immuneML.workflows.instructions.ligo_simulation immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction immuneML.workflows.instructions.ml_model_application immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction immuneML.workflows.instructions.ml_model_application.MLApplicationState immuneML.workflows.instructions.MLProcess immuneML.workflows.instructions.quickstart immuneML.workflows.instructions.subsampling immuneML.workflows.instructions.subsampling.SubsamplingInstruction immuneML.workflows.instructions.subsampling.SubsamplingState immuneML.workflows.instructions.train_gen_model immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction immuneML.workflows.instructions.TrainMLModelInstruction immuneML.workflows.steps immuneML.workflows.steps.data_splitter immuneML.workflows.steps.data_splitter.DataSplitter immuneML.workflows.steps.data_splitter.DataSplitterParams immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter immuneML.workflows.steps.data_splitter.ManualSplitter immuneML.workflows.steps.data_splitter.Util immuneML.workflows.steps.DataEncoder immuneML.workflows.steps.DataEncoderParams immuneML.workflows.steps.MLMethodAssessment immuneML.workflows.steps.MLMethodAssessmentParams immuneML.workflows.steps.MLMethodTrainer immuneML.workflows.steps.MLMethodTrainerParams immuneML.workflows.steps.Step immuneML.workflows.steps.StepParams

MORISITA (immuneML.analysis.similarities.SimilarityMeasureType.SimilarityMeasureType attribute) MORISITA_HORN (immuneML.encodings.distance_encoding.DistanceMetricType.DistanceMetricType attribute) morisita_horn() (in module immuneML.util.DistanceMetrics) Motif (class in immuneML.simulation.implants.Motif) MOTIF (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) motif_id (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) motif_instance (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) MotifInstance (class in immuneML.simulation.implants.MotifInstance) MotifInstanceGroup (class in immuneML.simulation.implants.MotifInstance) MotifParser (class in immuneML.dsl.definition_parsers.MotifParser) motifs (immuneML.simulation.implants.Signal.Signal attribute) MotifSeedRecovery (class in immuneML.reports.ml_reports.MotifSeedRecovery) MultiDatasetBenchmarkHTMLBuilder (class in immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder) MultiDatasetBenchmarkTool (class in immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool) MultiDatasetReport (class in immuneML.reports.multi_dataset_reports.MultiDatasetReport)

N

N_LARGEST (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) name (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.reports.ReportResult.ReportResult attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) NameBuilder (class in immuneML.util.NameBuilder) needs_seqs_with_signal() (in module immuneML.simulation.util.util) NONE (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute)

NONZERO (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) NormalizationType (class in immuneML.analysis.data_manipulation.NormalizationType) normalize() (immuneML.encodings.preprocessing.FeatureScaler.FeatureScaler static method) NOT_COMPUTED (immuneML.environment.Constants.Constants attribute) NOT_IN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) NOT_NA (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) NUCLEOTIDE (immuneML.environment.SequenceType.SequenceType attribute) NUM_DIGITS (immuneML.presentation.html.HPHTMLBuilder.HPHTMLBuilder attribute) number_of_processes (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) NumpyHelper (class in immuneML.util.NumpyHelper)

O

ObjectParser (class in immuneML.dsl.ObjectParser) OLGA (class in immuneML.ml_methods.generative_models.OLGA) olga_gen_model (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) OLGAImport (class in immuneML.IO.dataset_import.OLGAImport) OneHotEncoder (class in immuneML.encodings.onehot.OneHotEncoder) OneHotReceptorEncoder (class in immuneML.encodings.onehot.OneHotReceptorEncoder) OneHotRepertoireEncoder (class in immuneML.encodings.onehot.OneHotRepertoireEncoder) OneHotSequenceEncoder (class in immuneML.encodings.onehot.OneHotSequenceEncoder) OperationType (class in immuneML.analysis.criteria_matches.OperationType) optimal_assessment_item (immuneML.hyperparameter_optimization.states.HPLabelState.HPLabelState property) optimal_hp_item_paths (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) optimal_hp_items (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) optimal_hp_setting (immuneML.hyperparameter_optimization.states.HPLabelState.HPLabelState property) (immuneML.hyperparameter_optimization.states.HPSelectionState.HPSelectionState property) optimization_metric (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute)

OPTIONAL_KEYS (immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser attribute) OR (immuneML.analysis.criteria_matches.BooleanType.BooleanType attribute) organism (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) OTHER (immuneML.caching.CacheObjectType.CacheObjectType attribute) OUTPUT (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) OUTPUT_COLUMNS (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel attribute) (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) output_figures (immuneML.reports.ReportResult.ReportResult attribute) OUTPUT_FILENAME (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) output_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) output_pairs (immuneML.util.CompAIRRParams.CompAIRRParams attribute) output_tables (immuneML.reports.ReportResult.ReportResult attribute) output_text (immuneML.reports.ReportResult.ReportResult attribute) OutputParser (class in immuneML.dsl.OutputParser)

P

p_gen_histogram (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) pad_ragged_array() (in module immuneML.simulation.util.bnp_util) pad_sequence_in_the_middle() (immuneML.util.StringHelper.StringHelper static method) paired (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) pairs_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) PairwiseRepertoireComparison (class in immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison) parameter (immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig attribute) ParameterValidator (class in immuneML.util.ParameterValidator) parse() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser static method) (immuneML.dsl.definition_parsers.MLParser.MLParser static method) (immuneML.dsl.definition_parsers.MotifParser.MotifParser static method) (immuneML.dsl.definition_parsers.PreprocessingParser.PreprocessingParser static method) (immuneML.dsl.definition_parsers.ReportParser.ReportParser static method) (immuneML.dsl.definition_parsers.SignalParser.SignalParser static method) (immuneML.dsl.definition_parsers.SimulationParser.SimulationParser static method) (immuneML.dsl.ImmuneMLParser.ImmuneMLParser static method) (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) (immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser method) (immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser.ExploratoryAnalysisParser method) (immuneML.dsl.instruction_parsers.MLApplicationParser.MLApplicationParser method) (immuneML.dsl.instruction_parsers.SubsamplingParser.SubsamplingParser method) (immuneML.dsl.instruction_parsers.TrainMLModelParser.TrainMLModelParser method) (immuneML.dsl.InstructionParser.InstructionParser static method) (immuneML.dsl.OutputParser.OutputParser static method) (immuneML.dsl.Parser.Parser method) (immuneML.presentation.TemplateParser.TemplateParser static method) parse_adaptive_germline_to_imgt() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) parse_allele() (in module immuneML.util.AdaptiveImportHelper) parse_any_model() (immuneML.dsl.definition_parsers.MLParser.MLParser static method) parse_by_type() (immuneML.dsl.definition_parsers.MLParser.MLParser static method) parse_classifiers() (immuneML.dsl.definition_parsers.MLParser.MLParser static method) parse_criteria() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) parse_dataset() (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) parse_encoder() (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser static method) parse_gene_column() (in module immuneML.util.AdaptiveImportHelper) parse_germline() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) parse_instruction() (immuneML.dsl.InstructionParser.InstructionParser static method) parse_object() (immuneML.dsl.ObjectParser.ObjectParser static method) parse_parameters() (immuneML.util.SignificantFeaturesHelper.SignificantFeaturesHelper static method) parse_sequence_dataframe() (immuneML.util.ImportHelper.ImportHelper static method) parse_sequences_path() (immuneML.util.SignificantFeaturesHelper.SignificantFeaturesHelper static method) parse_yaml_file() (immuneML.dsl.ImmuneMLParser.ImmuneMLParser static method) Parser (class in immuneML.dsl.Parser) path (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) PathBuilder (class in immuneML.util.PathBuilder) paths (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) PEARSON (immuneML.analysis.similarities.SimilarityMeasureType.SimilarityMeasureType attribute) PERCENTAGE (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) performance (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) PerformanceOverview (class in immuneML.reports.multi_dataset_reports.PerformanceOverview) plot_inputs_text() (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery method) plot_kernels_text() (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery method) plot_precision_recall() (immuneML.reports.multi_dataset_reports.PerformanceOverview.PerformanceOverview method) plot_roc() (immuneML.reports.multi_dataset_reports.PerformanceOverview.PerformanceOverview method) PLOTLY_BLACK (immuneML.environment.Constants.Constants attribute)

PlotlyUtil (class in immuneML.reports.PlotlyUtil) pool_size (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) position (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) PositionHelper (class in immuneML.util.PositionHelper) positive_class (immuneML.environment.Label.Label property) PrecomputedKNN (class in immuneML.ml_methods.classifiers.PrecomputedKNN) predict() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) predict_proba() (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) predictions_path (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) prepare_caching_params() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) prepare_data_for_airr_seq_set() (in module immuneML.simulation.util.util) prepare_data_for_repertoire_obj() (in module immuneML.simulation.util.util) prepare_paralellization_arguments() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) prepare_path() (immuneML.workflows.steps.data_splitter.Util.Util static method) prepare_reference() (immuneML.encodings.reference_encoding.MatchedReferenceUtil.MatchedReferenceUtil static method) prepare_specs() (immuneML.api.galaxy.DataSimulationTool.DataSimulationTool method) prepare_tcr_dist_dataframe() (immuneML.util.TCRdistHelper.TCRdistHelper static method) prepare_training_ids() (immuneML.util.EncoderHelper.EncoderHelper static method) preprocess_dataframe() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) preprocess_dataset() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) preprocess_file() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IGoRImport.IGoRImport method) (immuneML.IO.dataset_import.ImmunoSEQRearrangementImport.ImmunoSEQRearrangementImport method) (immuneML.IO.dataset_import.ImmunoSEQSampleImport.ImmunoSEQSampleImport method) (immuneML.IO.dataset_import.MiXCRImport.MiXCRImport method) (immuneML.IO.dataset_import.TenxGenomicsImport.TenxGenomicsImport method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport method) PREPROCESSING (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) preprocessing_file (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) preprocessing_parameters (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) preprocessing_sequence (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) preprocessing_sequence_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) PreprocessingParser (class in immuneML.dsl.definition_parsers.PreprocessingParser) Preprocessor (class in immuneML.preprocessing.Preprocessor) PresentationFactory (class in immuneML.presentation.PresentationFactory) PresentationFormat (class in immuneML.presentation.PresentationFormat) print_log() (in module immuneML.util.Logger) print_performances() (immuneML.workflows.instructions.TrainMLModelInstruction.TrainMLModelInstruction method) ProbabilisticBinaryClassifier (class in immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier) process_compairr_output_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) process_dataset() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) (immuneML.preprocessing.filters.ChainRepertoireFilter.ChainRepertoireFilter method) (immuneML.preprocessing.filters.ClonesPerRepertoireFilter.ClonesPerRepertoireFilter method) (immuneML.preprocessing.filters.CountPerSequenceFilter.CountPerSequenceFilter method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter method) (immuneML.preprocessing.filters.MetadataRepertoireFilter.MetadataRepertoireFilter method) (immuneML.preprocessing.filters.SequenceLengthFilter.SequenceLengthFilter method) (immuneML.preprocessing.Preprocessor.Preprocessor method) (immuneML.preprocessing.ReferenceSequenceAnnotator.ReferenceSequenceAnnotator method) (immuneML.preprocessing.SubjectRepertoireCollector.SubjectRepertoireCollector method) process_repertoire() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) process_sequences() (immuneML.simulation.simulation_strategy.ImplantingStrategy.ImplantingStrategy method) (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy method) (immuneML.simulation.simulation_strategy.SimulationStrategy.SimulationStrategy method) PRODUCTION (immuneML.caching.CacheType.CacheType attribute) PWM (class in immuneML.ml_methods.generative_models.PWM) PyTorchLogisticRegression (class in immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression) PyTorchReceptorCNN (class in immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN) PyTorchSequenceDataset (class in immuneML.ml_methods.generative_models.SimpleVAE)

Q

Quickstart (class in immuneML.workflows.instructions.quickstart)

R

RANDOM (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) RANDOM_N (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) random_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) RandomDatasetGenerator (class in immuneML.simulation.dataset_generation.RandomDatasetGenerator) RandomForestClassifier (class in immuneML.ml_methods.classifiers.RandomForestClassifier) RandomReceptorDatasetImport (class in immuneML.IO.dataset_import.RandomReceptorDatasetImport) RandomRepertoireDatasetImport (class in immuneML.IO.dataset_import.RandomRepertoireDatasetImport) RandomSequenceDatasetImport (class in immuneML.IO.dataset_import.RandomSequenceDatasetImport) read_compairr_output_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) ReadsType (class in immuneML.util.ReadsType) receptor_chains (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) ReceptorCNN (class in immuneML.ml_methods.classifiers.ReceptorCNN) ReceptorDatasetOverview (class in immuneML.reports.data_reports.ReceptorDatasetOverview) RecoveredSignificantFeatures (class in immuneML.reports.data_reports.RecoveredSignificantFeatures) ReductionMethod (class in immuneML.analysis.data_manipulation.ReductionMethod) reeval_on_assessment_split() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) ReferenceSequenceAnnotator (class in immuneML.preprocessing.ReferenceSequenceAnnotator) ReferenceSequenceOverlap (class in immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap) refit_optimal_model (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) ReflectionHandler (class in immuneML.util.ReflectionHandler) reformat_galaxy_dataset() (immuneML.api.galaxy.Util.Util static method) region_type (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) REGRESSION (immuneML.environment.LabelType.LabelType attribute) RejectionSamplingStrategy (class in immuneML.simulation.simulation_strategy.RejectionSamplingStrategy) RELATIVE_ABUNDANCE (immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType.RelativeAbundanceType attribute) RELATIVE_FREQUENCY (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) RelativeAbundanceType (class in immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType) RELEVANT_SEQUENCE_ABUNDANCE (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder attribute) RelevantSequenceExporter (class in immuneML.reports.encoding_reports.RelevantSequenceExporter) remove_old_and_build() (immuneML.util.PathBuilder.PathBuilder static method) remove_path_from_filename() (immuneML.api.galaxy.Util.Util static method) renyi_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) repertoire_index_mapping (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) RepertoireBuilder (class in immuneML.util.RepertoireBuilder) RepertoireClassificationTool (class in immuneML.api.galaxy.RepertoireClassificationTool) RepertoireClonotypeSummary (class in immuneML.reports.data_reports.RepertoireClonotypeSummary) REPERTOIRES (immuneML.analysis.AxisType.AxisType attribute) REPERTOIRES_FOLDER (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport attribute) replace_nans_with_empty_str() (in module immuneML.util.AdaptiveImportHelper) Report (class in immuneML.reports.Report) REPORT (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) report (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) report_p_gen_histogram() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_result (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) report_results (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) report_seq_len_dist() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_cond_probs() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_cooccurrences() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_frequencies() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_joint_probs() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports)

ReportConfig (class in immuneML.hyperparameter_optimization.config.ReportConfig) ReportOutput (class in immuneML.reports.ReportOutput) ReportParser (class in immuneML.dsl.definition_parsers.ReportParser) ReportResult (class in immuneML.reports.ReportResult) reports (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) ReportUtil (class in immuneML.reports.ReportUtil) REQUIRED_KEYS (immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser attribute) rescale_weights_for_IGM() (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method) reset_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) reshape() (immuneML.analysis.data_manipulation.DataReshaper.DataReshaper static method) result_path (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) roc_auc_score() (in module immuneML.ml_metrics.ml_metrics) ROCCurve (class in immuneML.reports.ml_reports.ROCCurve) ROCCurveSummary (class in immuneML.reports.train_ml_model_reports.ROCCurveSummary) root_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) run() (immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool.MultiDatasetBenchmarkTool method) (immuneML.api.galaxy.GalaxyTool.GalaxyTool method) (immuneML.app.ImmuneMLApp.ImmuneMLApp method) (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) (immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction.DatasetExportInstruction method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) (immuneML.workflows.instructions.Instruction.Instruction method) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction method) (immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction.LigoSimInstruction method) (immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction.MLApplicationInstruction method) (immuneML.workflows.instructions.MLProcess.MLProcess method) (immuneML.workflows.instructions.quickstart.Quickstart method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelInstruction method) (immuneML.workflows.instructions.TrainMLModelInstruction.TrainMLModelInstruction method) (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) (immuneML.workflows.steps.DataEncoder.DataEncoder static method) (immuneML.workflows.steps.MLMethodAssessment.MLMethodAssessment static method) (immuneML.workflows.steps.MLMethodTrainer.MLMethodTrainer static method) (immuneML.workflows.steps.Step.Step static method) run_assessment() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) run_assessment_split() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) run_assessment_split_per_label() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) run_data_reports() (immuneML.reports.ReportUtil.ReportUtil static method) run_encoding_reports() (immuneML.reports.ReportUtil.ReportUtil static method) run_hyperparameter_reports() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) run_immuneML() (in module immuneML.app.ImmuneMLApp) run_instructions() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) run_ML_reports() (immuneML.reports.ReportUtil.ReportUtil static method) run_report() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) run_selection() (immuneML.hyperparameter_optimization.core.HPSelection.HPSelection static method) run_selection_reports() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) run_setting() (immuneML.hyperparameter_optimization.core.HPSelection.HPSelection static method) run_tool() (immuneML.api.galaxy.Util.Util static method) run_unit() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method)

S

save_model() (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SimpleVAE.SimpleVAE method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) scale_normalized() (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder method) score_for_metric() (immuneML.ml_metrics.MetricUtil.MetricUtil static method) selection (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) SemanticModel (class in immuneML.dsl.semantic_model.SemanticModel) SEP (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) separator (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) seq_len_dist (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) SEQUENCE (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) SEQUENCE_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) sequence_count (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) sequence_file_size (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) sequence_gen_model (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) sequence_position_weights (immuneML.simulation.implants.Signal.Signal attribute) sequence_type (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction.LigoSimInstruction property) SequenceAbundanceEncoder (class in immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder) SequenceAnalysisHelper (class in immuneML.util.SequenceAnalysisHelper) SequenceAssociationLikelihood (class in immuneML.reports.ml_reports.SequenceAssociationLikelihood) SequenceEncodingStrategy (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy) SequenceEncodingType (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType) SequenceLengthDistribution (class in immuneML.reports.data_reports.SequenceLengthDistribution) SequenceLengthFilter (class in immuneML.preprocessing.filters.SequenceLengthFilter) SequenceMatcher (class in immuneML.analysis.SequenceMatcher) SequenceMatchingSummaryType (class in immuneML.encodings.reference_encoding.SequenceMatchingSummaryType) SequenceModelCreator (class in immuneML.encodings.word2vec.model_creator.SequenceModelCreator) SequencesWithSignificantKmers (class in immuneML.reports.data_reports.SequencesWithSignificantKmers) SequenceType (class in immuneML.environment.SequenceType) set_background_probabilities() (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) set_cache() (immuneML.app.ImmuneMLApp.ImmuneMLApp method) set_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) set_context() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) (immuneML.encodings.distance_encoding.TCRdistEncoder.TCRdistEncoder method) (immuneML.reports.ml_reports.TCRdistMotifDiscovery.TCRdistMotifDiscovery method) (immuneML.reports.Report.Report method) set_iteration_repertoire_ids() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) set_locus_column() (in module immuneML.util.AdaptiveImportHelper) set_repertoire_ids() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) set_sequence_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) setup_pytorch() (immuneML.ml_methods.util.Util.Util static method) shannon_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) Signal (class in immuneML.simulation.implants.Signal) SIGNAL (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) signal1 (immuneML.simulation.implants.Signal.SignalPair attribute) signal2 (immuneML.simulation.implants.Signal.SignalPair attribute) signal_cond_probs (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) signal_cooccurrences (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) SIGNAL_DELIMITER (immuneML.environment.Constants.Constants attribute) signal_frequencies (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) signal_id (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) signal_joint_probs (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) SignalPair (class in immuneML.simulation.implants.Signal) SignalParser (class in immuneML.dsl.definition_parsers.SignalParser) signals (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) SignificantFeatures (class in immuneML.reports.data_reports.SignificantFeatures) SignificantFeaturesHelper (class in immuneML.util.SignificantFeaturesHelper) SignificantKmerPositions (class in immuneML.reports.data_reports.SignificantKmerPositions) SimilarityMeasureType (class in immuneML.analysis.similarities.SimilarityMeasureType) SIMPLE_TYPES (immuneML.util.NumpyHelper.NumpyHelper attribute)

SimpleDatasetOverview (class in immuneML.reports.data_reports.SimpleDatasetOverview) SimpleLSTM (class in immuneML.ml_methods.generative_models.SimpleLSTM) SimpleVAE (class in immuneML.ml_methods.generative_models.SimpleVAE) SIMULATION (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) simulation (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) SimulationParser (class in immuneML.dsl.definition_parsers.SimulationParser) SimulationStrategy (class in immuneML.simulation.simulation_strategy.SimulationStrategy) SKLEARN_NORMALIZATION_TYPES (immuneML.encodings.preprocessing.FeatureScaler.FeatureScaler attribute) SklearnMethod (class in immuneML.ml_methods.classifiers.SklearnMethod) SMALL_POSITIVE_NUMBER (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier attribute) software_used (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) SoNNia (class in immuneML.ml_methods.generative_models.SoNNia) source_docs_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) specs_docs_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) split_config (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) split_count (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) split_data() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) split_dataset() (immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter.LeaveOneOutSplitter static method) (immuneML.workflows.steps.data_splitter.ManualSplitter.ManualSplitter static method) split_index (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) split_strategy (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) SplitConfig (class in immuneML.hyperparameter_optimization.config.SplitConfig) SplitType (class in immuneML.hyperparameter_optimization.config.SplitType) standard_scale() (immuneML.encodings.preprocessing.FeatureScaler.FeatureScaler static method) standard_scale_fit() (immuneML.encodings.preprocessing.FeatureScaler.FeatureScaler static method) standardize_column_names() (immuneML.util.ImportHelper.ImportHelper static method) standardize_none_values() (immuneML.util.ImportHelper.ImportHelper static method) std() (immuneML.reports.encoding_reports.FeatureReport.FeatureReport method) (immuneML.reports.train_ml_model_reports.MLSettingsPerformance.MLSettingsPerformance method) Step (class in immuneML.workflows.steps.Step) STEP (immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood attribute) STEP_ENCODED (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder attribute) STEP_NORMALIZED (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder attribute) STEP_SCALED (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder attribute) STEP_VECTORIZED (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder attribute) StepParams (class in immuneML.workflows.steps.StepParams) STOP_CODON (immuneML.environment.Constants.Constants attribute) store() (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.ml_methods.classifiers.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.classifiers.DeepRC.DeepRC method) (immuneML.ml_methods.classifiers.MLMethod.MLMethod method) (immuneML.ml_methods.classifiers.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.classifiers.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.classifiers.SklearnMethod.SklearnMethod method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) (immuneML.workflows.steps.MLMethodTrainer.MLMethodTrainer static method) store_encoder() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) store_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) strategy_supports_signals() (in module immuneML.dsl.definition_parsers.SimulationParser) STRATIFIED_K_FOLD (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) stratified_k_fold_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) StringHelper (class in immuneML.util.StringHelper) SubjectRepertoireCollector (class in immuneML.preprocessing.SubjectRepertoireCollector) subsampled_dataset_paths (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) subsampled_dataset_sizes (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) subsampled_datasets (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) SubsamplingHTMLBuilder (class in immuneML.presentation.html.SubsamplingHTMLBuilder) SubsamplingInstruction (class in immuneML.workflows.instructions.subsampling.SubsamplingInstruction) SubsamplingParser (class in immuneML.dsl.instruction_parsers.SubsamplingParser) SubsamplingState (class in immuneML.workflows.instructions.subsampling.SubsamplingState) subset_encoded_data() (immuneML.ml_methods.util.Util.Util static method) SUM (immuneML.analysis.data_manipulation.ReductionMethod.ReductionMethod attribute) (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) SVC (class in immuneML.ml_methods.classifiers.SVC) SVM (class in immuneML.ml_methods.classifiers.SVM) SymbolTable (class in immuneML.dsl.symbol_table.SymbolTable) SymbolTableEntry (class in immuneML.dsl.symbol_table.SymbolTableEntry) SymbolType (class in immuneML.dsl.symbol_table.SymbolType) sync_encoder_with_cache() (immuneML.util.EncoderHelper.EncoderHelper static method)

T

TCRB_RELATIVE_ABUNDANCE (immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType.RelativeAbundanceType attribute) TCRdistClassifier (class in immuneML.ml_methods.classifiers.TCRdistClassifier) TCRdistEncoder (class in immuneML.encodings.distance_encoding.TCRdistEncoder) TCRdistHelper (class in immuneML.util.TCRdistHelper) TCRdistMotifDiscovery (class in immuneML.reports.ml_reports.TCRdistMotifDiscovery) TemplateParser (class in immuneML.presentation.TemplateParser) TenxGenomicsImport (class in immuneML.IO.dataset_import.TenxGenomicsImport) TEST (immuneML.caching.CacheType.CacheType attribute) test_dataset (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) test_metadata_path (immuneML.hyperparameter_optimization.config.ManualSplitConfig.ManualSplitConfig attribute) test_predictions_path (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) threads (immuneML.util.CompAIRRParams.CompAIRRParams attribute) tmp_cache_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) tmp_test_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) to_dict_recursive() (immuneML.presentation.html.Util.Util static method) TOP_N (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) TOTAL_SEQUENCE_ABUNDANCE (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.KmerAbundanceEncoder.KmerAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder attribute)

train_dataset (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) train_dataset_id (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) train_dataset_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) train_metadata_path (immuneML.hyperparameter_optimization.config.ManualSplitConfig.ManualSplitConfig attribute) train_predictions_path (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) TrainGenModelInstruction (class in immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction) TrainGenModelState (class in immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction) training_percentage (immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction.TrainGenModelState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) TrainingPerformance (class in immuneML.reports.ml_reports.TrainingPerformance) TrainMLModelInstruction (class in immuneML.workflows.instructions.TrainMLModelInstruction) TrainMLModelParser (class in immuneML.dsl.instruction_parsers.TrainMLModelParser) TrainMLModelReport (class in immuneML.reports.train_ml_model_reports.TrainMLModelReport) TrainMLModelState (class in immuneML.hyperparameter_optimization.states.TrainMLModelState) translate_sequence() (immuneML.IO.dataset_import.IGoRImport.IGoRImport static method)

U

UNIQUE (immuneML.util.ReadsType.ReadsType attribute) UNKNOWN (immuneML.environment.Constants.Constants attribute) UNKNOWN_CHAIN (immuneML.reports.data_reports.SimpleDatasetOverview.SimpleDatasetOverview attribute) update_dataset_key() (immuneML.api.galaxy.Util.Util static method) update_hp_setting_for_assessment() (immuneML.hyperparameter_optimization.core.HPAssessment.HPAssessment static method) update_report_paths() (immuneML.presentation.html.Util.Util static method) update_result_paths() (immuneML.api.galaxy.Util.Util static method) update_seqs_with_signal() (in module immuneML.simulation.util.util) update_seqs_without_signal() (in module immuneML.simulation.util.util)

update_specs() (immuneML.api.galaxy.GalaxyYamlTool.GalaxyYamlTool method) update_split_by_label_kwargs() (immuneML.reports.ReportUtil.ReportUtil static method) update_split_count() (immuneML.hyperparameter_optimization.core.HPSelection.HPSelection static method) Util (class in immuneML.api.galaxy.Util) (class in immuneML.encodings.atchley_kmer_encoding.Util) (class in immuneML.ml_methods.util.Util) (class in immuneML.presentation.html.Util) (class in immuneML.workflows.steps.data_splitter.Util) UtilIO (class in immuneML.IO.ml_method.UtilIO)

V

v_call (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) v_gene_mapping (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) VAESummary (class in immuneML.reports.gen_model_reports.VAESummary)

valid_keys (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute) values (immuneML.environment.Label.Label property) VDJdbImport (class in immuneML.IO.dataset_import.VDJdbImport) verify_compairr_output_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) VERSION (immuneML.environment.Constants.Constants attribute)

W

W2VRepertoireEncoder (class in immuneML.encodings.word2vec.W2VRepertoireEncoder) W2VSequenceEncoder (class in immuneML.encodings.word2vec.W2VSequenceEncoder) warnings (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) weight_examples() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method)

WEIGHTING (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) Word2VecEncoder (class in immuneML.encodings.word2vec.Word2VecEncoder) write_bnp_data() (in module immuneML.simulation.util.util) write_repertoire_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) write_sequence_set_file() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) write_sequences_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method)