Index

A

ACCURACY (immuneML.ml_metrics.Metric.Metric attribute) 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_default_allele_to_v_gene() (immuneML.util.TCRdistHelper.TCRdistHelper static method) add_encoded_data() (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) add_implant() (immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation.SequenceAnnotation 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) adjust_position_weights() (immuneML.util.PositionHelper.PositionHelper 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) 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)

ALPHA (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) alternative_load_func() (immuneML.IO.dataset_import.AIRRImport.AIRRImport static method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport static method) AMINO_ACID (immuneML.environment.SequenceType.SequenceType attribute) AND (immuneML.analysis.criteria_matches.BooleanType.BooleanType attribute) assert_all_in_valid_list() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_all_type_and_value() (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_type_and_value() (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) 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.AtchleyKmerMILClassifier) AUC (immuneML.ml_metrics.Metric.Metric attribute) AVG (immuneML.analysis.data_manipulation.ReductionMethod.ReductionMethod attribute) AxisType (class in immuneML.analysis.AxisType)

B

BALANCED_ACCURACY (immuneML.ml_metrics.Metric.Metric attribute) BCKReceptor (class in immuneML.data_model.receptor.BCKReceptor) BCReceptor (class in immuneML.data_model.receptor.BCReceptor) BETA (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) 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.data_model.dataset.ReceptorDataset.ReceptorDataset class method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset class method) (immuneML.data_model.dataset.SequenceDataset.SequenceDataset class method) (immuneML.data_model.repertoire.Repertoire.Repertoire class method) (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.SimulationHTMLBuilder.SimulationHTMLBuilder static method) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder static method) (immuneML.util.PathBuilder.PathBuilder static method) (immuneML.util.RepertoireBuilder.RepertoireBuilder static method) build_batch_generator() (immuneML.data_model.receptor.ElementGenerator.ElementGenerator method) build_comparison_data() (immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper.SequenceFilterHelper static method) (immuneML.util.EncoderHelper.EncoderHelper static method) build_comparison_params() (immuneML.util.EncoderHelper.EncoderHelper static method) build_distance_matrix() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) build_element_generator() (immuneML.data_model.receptor.ElementGenerator.ElementGenerator method) build_encodings_specs() (in module immuneML.api.galaxy.build_yaml_from_arguments) build_from_objects() (immuneML.data_model.dataset.Dataset.Dataset class method) (immuneML.data_model.dataset.ReceptorDataset.ReceptorDataset class method) (immuneML.data_model.dataset.SequenceDataset.SequenceDataset class method) build_from_sequence_objects() (immuneML.data_model.repertoire.Repertoire.Repertoire class method) build_labels() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) (in module immuneML.api.galaxy.build_yaml_from_arguments) build_like() (immuneML.data_model.repertoire.Repertoire.Repertoire class method) build_matching_fn() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) build_metadata_column_mapping() (in module immuneML.api.galaxy.build_dataset_yaml) build_ml_methods_specs() (in module immuneML.api.galaxy.build_yaml_from_arguments) build_name_from_dict() (immuneML.util.NameBuilder.NameBuilder static method) build_object() (immuneML.data_model.receptor.ReceptorBuilder.ReceptorBuilder class 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.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder 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.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter class method) (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter class method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter class method) (immuneML.reports.data_reports.ReceptorDatasetOverview.ReceptorDatasetOverview class method) (immuneML.reports.data_reports.SequenceLengthDistribution.SequenceLengthDistribution 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.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.MLSubseqPerformance.MLSubseqPerformance class method) (immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap.ReferenceSequenceOverlap class method) (immuneML.reports.train_ml_model_reports.ROCCurveSummary.ROCCurveSummary class method)

build_objects() (immuneML.data_model.receptor.ReceptorBuilder.ReceptorBuilder class method) build_path() (immuneML.workflows.instructions.quickstart.Quickstart method) build_position_weights() (immuneML.util.PositionHelper.PositionHelper static method) build_receptor_from_rows() (immuneML.util.ImportHelper.ImportHelper static method) build_reports() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) build_settings_specs() (in module immuneML.api.galaxy.build_yaml_from_arguments) build_specs() (in module immuneML.api.galaxy.build_dataset_yaml) (in module immuneML.api.galaxy.build_yaml_from_arguments)

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_predict_proba() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.KNN.KNN method) (immuneML.ml_methods.LogisticRegression.LogisticRegression method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.RandomForestClassifier.RandomForestClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.SVC.SVC method) (immuneML.ml_methods.SVM.SVM method) (immuneML.ml_methods.TCRdistClassifier.TCRdistClassifier method) Cell (class in immuneML.data_model.cell.Cell) CellList (class in immuneML.data_model.cell.CellList) cells (immuneML.data_model.repertoire.Repertoire.Repertoire property) Chain (class in immuneML.data_model.receptor.receptor_sequence.Chain) ChainPair (class in immuneML.data_model.receptor.ChainPair) ChainRepertoireFilter (class in immuneML.preprocessing.filters.ChainRepertoireFilter) check() (immuneML.data_model.cell.CellList.CellList method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList.ReceptorSequenceList method) (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) check_arguments() (in module immuneML.api.galaxy.build_yaml_from_arguments) check_compairr_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) check_count() (immuneML.data_model.repertoire.Repertoire.Repertoire static method) check_dataset_not_empty() (immuneML.preprocessing.filters.Filter.Filter method) check_dataset_type() (immuneML.preprocessing.Preprocessor.Preprocessor method) check_encoder_compatibility() (immuneML.ml_methods.MLMethod.MLMethod method) check_export_format() (immuneML.api.galaxy.Util.Util static method) check_if_exists() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) check_instruction_type() (immuneML.api.galaxy.Util.Util static method) check_is_fitted() (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) check_keys() (immuneML.dsl.ImmuneMLParser.ImmuneMLParser static method) check_label_format() (immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper static method) check_parameters() (immuneML.api.galaxy.Util.Util static method) check_paths() (immuneML.api.galaxy.Util.Util static method) check_positive_class_label() (immuneML.util.EncoderHelper.EncoderHelper static method) check_prerequisites() (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter method) (immuneML.reports.data_reports.ReceptorDatasetOverview.ReceptorDatasetOverview method) (immuneML.reports.data_reports.SequenceLengthDistribution.SequenceLengthDistribution 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.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.MLSubseqPerformance.MLSubseqPerformance method) (immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap.ReferenceSequenceOverlap method) CLASSIFICATION (immuneML.environment.LabelType.LabelType attribute) clear_cache() (immuneML.app.ImmuneMLApp.ImmuneMLApp method) CLONAL_PERCENTAGE (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) clone() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.ReceptorDataset.ReceptorDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) (immuneML.data_model.dataset.SequenceDataset.SequenceDataset method) (immuneML.data_model.receptor.Receptor.Receptor method) (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 (immuneML.reports.encoding_reports.RelevantSequenceExporter.RelevantSequenceExporter attribute) column_mapping_synonyms (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) columns_to_load (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) COMMENT_SIGN (immuneML.environment.Constants.Constants attribute) compairr_path (immuneML.util.CompAIRRParams.CompAIRRParams attribute) 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.filtered_sequence_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) compute_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_contributions() (immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery method) compute_cosine() (immuneML.analysis.similarities.RepertoireSimilarityComputer.RepertoireSimilarityComputer static method) compute_jaccard() (immuneML.analysis.similarities.RepertoireSimilarityComputer.RepertoireSimilarityComputer static method) compute_morisita() (immuneML.analysis.similarities.RepertoireSimilarityComputer.RepertoireSimilarityComputer static method) compute_overlap_matrix() (immuneML.util.SequenceAnalysisHelper.SequenceAnalysisHelper static method) compute_pearson() (immuneML.analysis.similarities.RepertoireSimilarityComputer.RepertoireSimilarityComputer static method) compute_relative_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static 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) CONFUSION_MATRIX (immuneML.ml_metrics.Metric.Metric attribute) Constants (class in immuneML.environment.Constants) 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_from_record() (immuneML.data_model.receptor.BCKReceptor.BCKReceptor class method) (immuneML.data_model.receptor.BCReceptor.BCReceptor class method) (immuneML.data_model.receptor.Receptor.Receptor class method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence class method) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor class method) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor class 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_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) create_specs_defs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static 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.SimulationHTMLBuilder.SimulationHTMLBuilder attribute) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder attribute) CUTOFF (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) CVFeaturePerformance (class in immuneML.reports.train_ml_model_reports.CVFeaturePerformance) CytoscapeNetworkExporter (class in immuneML.reports.data_reports.CytoscapeNetworkExporter)

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 (class in immuneML.data_model.dataset.Dataset) DATASET (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) dataset (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) (immuneML.simulation.SimulationState.SimulationState 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_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.reference_encoding.MatchedSequencesEncoder.MatchedSequencesEncoder attribute) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder attribute) DATASET_NAME (immuneML.workflows.steps.SignalImplanter.SignalImplanter 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)

DatasetItem (class in immuneML.data_model.DatasetItem) 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.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_parameters (immuneML.ml_methods.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) DELTA (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) 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) discover_classes_by_partial_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) discover_dataset_params() (in module immuneML.api.galaxy.build_yaml_from_arguments) 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) DocEnumHelper (class in immuneML.util.DocEnumHelper) 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

ElementDataset (class in immuneML.data_model.dataset.ElementDataset) ElementGenerator (class in immuneML.data_model.receptor.ElementGenerator) encode() (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.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder 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) encode_dataset_by_kmer_freq() (in module immuneML.api.api_encoding) encode_labels (immuneML.encodings.EncoderParams.EncoderParams attribute) encode_repertoire() (immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder.EvennessProfileRepertoireEncoder method) (immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder.KmerFreqRepertoireEncoder 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) EncodedData (class in immuneML.data_model.encoded_data.EncodedData) 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) exists() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.util.ReflectionHandler.ReflectionHandler static method) 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.dataset_export.ImmuneMLExporter.ImmuneMLExporter static method) (immuneML.IO.ml_method.MLExporter.MLExporter static method) export_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_dataset() (immuneML.workflows.instructions.SimulationInstruction.SimulationInstruction method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) export_encoder() (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder 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.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder static method) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder static method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder static method) export_metadata_file() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) export_pairwise_comparison() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_receptorlist() (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter method) export_repertoire_tsv_files() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) export_updated_metadata() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) export_zip() (immuneML.IO.ml_method.MLExporter.MLExporter static method) EXTENSION (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) extract_meta_columns() (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) extract_sequence_dataset_params() (immuneML.util.ImportHelper.ImportHelper static method)

F

F1_MACRO (immuneML.ml_metrics.Metric.Metric attribute) F1_MICRO (immuneML.ml_metrics.Metric.Metric attribute) 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) F1_WEIGHTED (immuneML.ml_metrics.Metric.Metric attribute) 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) FIELDS (immuneML.data_model.receptor.BCKReceptor.BCKReceptor attribute) (immuneML.data_model.receptor.BCReceptor.BCReceptor attribute) (immuneML.data_model.receptor.Receptor.Receptor attribute) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence attribute) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor attribute) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor attribute) (immuneML.data_model.repertoire.Repertoire.Repertoire attribute) filename (immuneML.encodings.EncoderParams.EncoderParams 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_sequences() (immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper.SequenceFilterHelper static method) find_label_associated_sequence_p_values() (immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper.SequenceFilterHelper static method) FIRST (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) FIT (immuneML.ml_methods.SklearnMethod.SklearnMethod attribute) fit() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) fit_by_cross_validation() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) FIT_CV (immuneML.ml_methods.SklearnMethod.SklearnMethod attribute) formats (immuneML.simulation.SimulationState.SimulationState attribute) (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) free_memory() (immuneML.data_model.repertoire.Repertoire.Repertoire method) FULL_SEQUENCE (immuneML.data_model.receptor.RegionType.RegionType attribute) FullSequenceImplanting (class in immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting)

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) GAMMA (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) GappedKmerInstantiation (class in immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation) GappedKmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder) GappedMotifImplanting (class in immuneML.simulation.sequence_implanting.GappedMotifImplanting) 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_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) GenericImport (class in immuneML.IO.dataset_import.GenericImport) get() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_additional_files() (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder 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_params() (immuneML.dsl.ObjectParser.ObjectParser static method) get_atchely_factors() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) get_attribute() (immuneML.data_model.DatasetItem.DatasetItem method) (immuneML.data_model.receptor.BCKReceptor.BCKReceptor method) (immuneML.data_model.receptor.BCReceptor.BCReceptor method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence method) (immuneML.data_model.receptor.receptor_sequence.SequenceMetadata.SequenceMetadata method) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor method) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor method) (immuneML.data_model.repertoire.Repertoire.Repertoire method) get_attributes() (immuneML.data_model.repertoire.Repertoire.Repertoire method) get_auxiliary_labels() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_average_performance() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) get_batch() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_batches() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) 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_chain() (immuneML.data_model.receptor.Receptor.Receptor method) (immuneML.data_model.receptor.receptor_sequence.Chain.Chain static method) get_chain_for_row() (immuneML.util.ImportHelper.ImportHelper static method) get_chain_pair() (immuneML.data_model.receptor.ChainPair.ChainPair static method) get_chains() (immuneML.data_model.receptor.BCKReceptor.BCKReceptor method) (immuneML.data_model.receptor.BCReceptor.BCReceptor method) (immuneML.data_model.receptor.Receptor.Receptor method) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor method) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor method) (immuneML.data_model.repertoire.Repertoire.Repertoire 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_mapping() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) get_class_name() (immuneML.dsl.ObjectParser.ObjectParser static method) get_classes() (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier 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.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.KNN.KNN method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.TCRdistClassifier.TCRdistClassifier method) get_config() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_counts() (immuneML.data_model.repertoire.Repertoire.Repertoire method) get_css_content() (immuneML.presentation.html.Util.Util static method) get_current_dataset() (immuneML.util.EncoderHelper.EncoderHelper static method) get_data() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_dataset_name() (immuneML.util.FilenameHandler.FilenameHandler static 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.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder 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.MiXCRImport.MiXCRImport static method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport static method) (immuneML.IO.dataset_import.SingleLineReceptorImport.SingleLineReceptorImport static method) (immuneML.IO.dataset_import.TenxGenomicsImport.TenxGenomicsImport static method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) (immuneML.ml_methods.KNN.KNN static method) (immuneML.ml_methods.LogisticRegression.LogisticRegression static method) (immuneML.ml_methods.PrecomputedKNN.PrecomputedKNN static method) (immuneML.ml_methods.RandomForestClassifier.RandomForestClassifier static method) (immuneML.ml_methods.SVC.SVC static method) (immuneML.ml_methods.SVM.SVM static method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter static method) (immuneML.reports.ml_reports.Coefficients.Coefficients static method) (immuneML.simulation.implants.Motif.Motif static method) (immuneML.simulation.implants.Signal.Signal static method) (immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction.DatasetExportInstruction static method) (immuneML.workflows.instructions.SimulationInstruction.SimulationInstruction static method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction static method) (immuneML.workflows.instructions.TrainMLModelInstruction.TrainMLModelInstruction static method) get_element_count() (immuneML.data_model.receptor.ElementGenerator.ElementGenerator method) (immuneML.data_model.repertoire.Repertoire.Repertoire 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_count() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_example_ids() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset 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.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) get_file_path() (immuneML.caching.CacheHandler.CacheHandler static method) get_filename() (immuneML.util.FilenameHandler.FilenameHandler static method) get_filenames() (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_formatted_edge_metadata() (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter method) get_formatted_node_metadata() (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter method) get_full_specs_path() (immuneML.presentation.html.Util.Util static method) get_immuneML_version() (immuneML.ml_methods.util.Util.Util static method) get_implanting_function() (in module immuneML.simulation.signal_implanting_strategy.ImplantingComputation) 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.data_model.repertoire.Repertoire.Repertoire 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.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) get_label_names() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset 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_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) get_max_gap() (immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation.GappedKmerInstantiation method) (immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy.MotifInstantiationStrategy method) get_max_information_gain() (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method) get_max_length() (immuneML.simulation.implants.Motif.Motif method) get_metadata() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ReceptorDataset.ReceptorDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) (immuneML.data_model.dataset.SequenceDataset.SequenceDataset method) get_metadata_fields() (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_ml_method_spec() (in module immuneML.api.galaxy.build_yaml_from_arguments) get_model_name() (immuneML.util.FilenameHandler.FilenameHandler static method) 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.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) get_params() (immuneML.dsl.ObjectParser.ObjectParser static method) (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.KNN.KNN method) (immuneML.ml_methods.LogisticRegression.LogisticRegression method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.PrecomputedKNN.PrecomputedKNN method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.RandomForestClassifier.RandomForestClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) (immuneML.ml_methods.SVC.SVC method) (immuneML.ml_methods.SVM.SVM method) (immuneML.ml_methods.TCRdistClassifier.TCRdistClassifier method) get_performance() (immuneML.hyperparameter_optimization.strategy.GridSearch.GridSearch method) get_probability_based_metric_types() (immuneML.ml_metrics.Metric.Metric static method) get_record() (immuneML.data_model.receptor.Receptor.Receptor method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence method) get_record_names() (immuneML.data_model.receptor.BCKReceptor.BCKReceptor class method) (immuneML.data_model.receptor.BCReceptor.BCReceptor class method) (immuneML.data_model.receptor.Receptor.Receptor class method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence class method) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor class method) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor class method) get_relevant_sequence_attributes() (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_relevant_sequences() (immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper.SequenceFilterHelper static method) get_repertoire() (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_repertoire_contents() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) get_repertoire_ids() (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) get_repertoire_vector() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_repertoire_vectors() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_search_criterion() (immuneML.ml_metrics.Metric.Metric static method) get_sequence() (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence method) get_sequence_aa_field() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) get_sequence_aas() (immuneML.data_model.repertoire.Repertoire.Repertoire method) get_sequence_alphabet() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_sequence_enc_type() (in module immuneML.api.galaxy.build_yaml_from_arguments) get_sequence_field() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) get_sequence_filenames() (immuneML.util.ImportHelper.ImportHelper static method) get_sequence_identifiers() (immuneML.data_model.repertoire.Repertoire.Repertoire method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) get_sequence_objects() (immuneML.data_model.repertoire.Repertoire.Repertoire method) get_sequence_set() (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_sequence_set_for_repertoire() (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_sequence_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_shared_name() (immuneML.reports.data_reports.CytoscapeNetworkExporter.CytoscapeNetworkExporter method) get_sklearn_score_name() (immuneML.ml_metrics.Metric.Metric 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_title() (immuneML.reports.data_reports.DataReport.DataReport static method) (immuneML.reports.encoding_reports.EncodingReport.EncodingReport static method) (immuneML.reports.ml_reports.MLReport.MLReport static method) (immuneML.reports.multi_dataset_reports.MultiDatasetReport.MultiDatasetReport static method) (immuneML.reports.train_ml_model_reports.TrainMLModelReport.TrainMLModelReport static method) get_tmp_batches() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_usage_documentation() (immuneML.ml_methods.SklearnMethod.SklearnMethod static method) get_v_genes() (immuneML.data_model.repertoire.Repertoire.Repertoire 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) HealthySequenceImplanting (class in immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting) HEAVY (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) 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_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) IGH_IGK (immuneML.data_model.receptor.ChainPair.ChainPair attribute) IGH_IGL (immuneML.data_model.receptor.ChainPair.ChainPair attribute) ignore_counts (immuneML.util.CompAIRRParams.CompAIRRParams attribute) ignore_genes (immuneML.util.CompAIRRParams.CompAIRRParams attribute) IGoRImport (class in immuneML.IO.dataset_import.IGoRImport) IMGT_CDR1 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_CDR2 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_CDR3 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_CONTINUOUS_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGT_FR1 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_FR2 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_FR3 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_FR4 (immuneML.data_model.receptor.RegionType.RegionType attribute) IMGT_GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGT_JUNCTION (immuneML.data_model.receptor.RegionType.RegionType 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.RepertoireSimilarityComputer 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.build_dataset_yaml module immuneML.api.galaxy.build_yaml_from_arguments 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.data_model.cell module immuneML.data_model.cell.Cell module immuneML.data_model.cell.CellList module immuneML.data_model.dataset module immuneML.data_model.dataset.Dataset module immuneML.data_model.dataset.ElementDataset module immuneML.data_model.dataset.ReceptorDataset module immuneML.data_model.dataset.RepertoireDataset module immuneML.data_model.dataset.SequenceDataset module immuneML.data_model.DatasetItem module immuneML.data_model.encoded_data module immuneML.data_model.encoded_data.EncodedData module immuneML.data_model.receptor module immuneML.data_model.receptor.BCKReceptor module immuneML.data_model.receptor.BCReceptor module immuneML.data_model.receptor.ChainPair module immuneML.data_model.receptor.ElementGenerator module immuneML.data_model.receptor.Receptor module immuneML.data_model.receptor.receptor_sequence module immuneML.data_model.receptor.receptor_sequence.Chain module immuneML.data_model.receptor.receptor_sequence.ReceptorSequence module immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList module immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation module immuneML.data_model.receptor.receptor_sequence.SequenceFrameType module immuneML.data_model.receptor.receptor_sequence.SequenceMetadata module immuneML.data_model.receptor.ReceptorBuilder module immuneML.data_model.receptor.RegionType module immuneML.data_model.receptor.TCABReceptor module immuneML.data_model.receptor.TCGDReceptor module immuneML.data_model.repertoire module immuneML.data_model.repertoire.Repertoire 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.SimulationParser 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.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.filtered_sequence_encoding module immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder module immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder module immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper 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.MatchedReceptorsRepertoireEncoder 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.MatchedSequencesRepertoireEncoder 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.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_export.ImmuneMLExporter 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.ImmuneMLImport 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.SingleLineReceptorImport 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.AtchleyKmerMILClassifier module immuneML.ml_methods.DeepRC module immuneML.ml_methods.KNN module immuneML.ml_methods.LogisticRegression module immuneML.ml_methods.MLMethod module immuneML.ml_methods.PrecomputedKNN module immuneML.ml_methods.ProbabilisticBinaryClassifier module immuneML.ml_methods.pytorch_implementations module immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module immuneML.ml_methods.RandomForestClassifier module immuneML.ml_methods.ReceptorCNN module immuneML.ml_methods.SklearnMethod module immuneML.ml_methods.SVC module immuneML.ml_methods.SVM module immuneML.ml_methods.TCRdistClassifier module immuneML.ml_methods.util module immuneML.ml_methods.util.Util module immuneML.ml_metrics module immuneML.ml_metrics.Metric 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.Preprocessor 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.SimulationHTMLBuilder 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.CytoscapeNetworkExporter module immuneML.reports.data_reports.DataReport module immuneML.reports.data_reports.GLIPH2Exporter module immuneML.reports.data_reports.ReceptorDatasetOverview module immuneML.reports.data_reports.SequenceLengthDistribution 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.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.MLSubseqPerformance 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.Implanting 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.motif_instantiation_strategy.GappedKmerInstantiation module immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy module immuneML.simulation.sequence_implanting module immuneML.simulation.sequence_implanting.GappedMotifImplanting module immuneML.simulation.sequence_implanting.SequenceImplantingStrategy module immuneML.simulation.signal_implanting_strategy module immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting module immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting module immuneML.simulation.signal_implanting_strategy.ImplantingComputation module immuneML.simulation.signal_implanting_strategy.ReceptorImplanting module immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy module immuneML.simulation.Simulation module immuneML.simulation.SimulationState 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.ReflectionHandler module immuneML.util.RepertoireBuilder module immuneML.util.SequenceAnalysisHelper 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.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.SimulationInstruction module immuneML.workflows.instructions.subsampling module immuneML.workflows.instructions.subsampling.SubsamplingInstruction module immuneML.workflows.instructions.subsampling.SubsamplingState 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.SignalImplanter module immuneML.workflows.steps.Step module immuneML.workflows.steps.StepParams module ImmuneMLApp (class in immuneML.app.ImmuneMLApp) ImmuneMLExporter (class in immuneML.IO.dataset_export.ImmuneMLExporter) ImmuneMLImport (class in immuneML.IO.dataset_import.ImmuneMLImport) ImmuneMLParser (class in immuneML.dsl.ImmuneMLParser) ImmunoSEQRearrangementImport (class in immuneML.IO.dataset_import.ImmunoSEQRearrangementImport) ImmunoSEQSampleImport (class in immuneML.IO.dataset_import.ImmunoSEQSampleImport) implant() (immuneML.simulation.sequence_implanting.GappedMotifImplanting.GappedMotifImplanting method) (immuneML.simulation.sequence_implanting.SequenceImplantingStrategy.SequenceImplantingStrategy method) implant_in_receptor() (immuneML.simulation.implants.Signal.Signal method) (immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting.FullSequenceImplanting method) (immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting.HealthySequenceImplanting method) (immuneML.simulation.signal_implanting_strategy.ReceptorImplanting.ReceptorImplanting method) (immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy.SignalImplantingStrategy method) implant_in_repertoire() (immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting.FullSequenceImplanting method) (immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting.HealthySequenceImplanting method) (immuneML.simulation.signal_implanting_strategy.ReceptorImplanting.ReceptorImplanting method) (immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy.SignalImplantingStrategy method) implant_in_sequence() (immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy.SignalImplantingStrategy method) implant_to_repertoire() (immuneML.simulation.implants.Signal.Signal method) ImplantAnnotation (class in immuneML.simulation.implants.ImplantAnnotation) Implanting (class in immuneML.simulation.Implanting) ImplantingComputation (class in immuneML.simulation.signal_implanting_strategy.ImplantingComputation) import_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) import_dataset() (immuneML.IO.dataset_import.AIRRImport.AIRRImport static method) (immuneML.IO.dataset_import.DataImport.DataImport static method) (immuneML.IO.dataset_import.GenericImport.GenericImport static method) (immuneML.IO.dataset_import.IGoRImport.IGoRImport static method) (immuneML.IO.dataset_import.ImmuneMLImport.ImmuneMLImport 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.MiXCRImport.MiXCRImport static method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport static method) (immuneML.IO.dataset_import.RandomReceptorDatasetImport.RandomReceptorDatasetImport static method) (immuneML.IO.dataset_import.RandomRepertoireDatasetImport.RandomRepertoireDatasetImport static method) (immuneML.IO.dataset_import.RandomSequenceDatasetImport.RandomSequenceDatasetImport static method) (immuneML.IO.dataset_import.SingleLineReceptorImport.SingleLineReceptorImport static method) (immuneML.IO.dataset_import.TenxGenomicsImport.TenxGenomicsImport static method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) (immuneML.util.ImportHelper.ImportHelper static 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_items() (immuneML.util.ImportHelper.ImportHelper 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_receptors() (immuneML.IO.dataset_import.AIRRImport.AIRRImport static method) (immuneML.IO.dataset_import.GenericImport.GenericImport static method) (immuneML.IO.dataset_import.TenxGenomicsImport.TenxGenomicsImport static method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) (immuneML.util.ImportHelper.ImportHelper static method) import_receptors_by_id() (immuneML.util.ImportHelper.ImportHelper static method) import_repertoire_dataset() (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport static method) (immuneML.util.ImportHelper.ImportHelper static method) import_sequence() (immuneML.util.ImportHelper.ImportHelper static method) import_sequence_dataset() (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport static method) (immuneML.util.ImportHelper.ImportHelper static method) 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) (immuneML.data_model.receptor.receptor_sequence.SequenceFrameType.SequenceFrameType attribute) indels (immuneML.util.CompAIRRParams.CompAIRRParams attribute) info (immuneML.reports.ReportResult.ReportResult attribute) INPUT_FILENAME (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) insert() (immuneML.data_model.cell.CellList.CellList method) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList.ReceptorSequenceList method) (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) instantiate() (immuneML.analysis.criteria_matches.CriteriaTypeInstantiator.CriteriaTypeInstantiator static method) instantiate_motif() (immuneML.simulation.implants.Motif.Motif method) (immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation.GappedKmerInstantiation method) (immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy.MotifInstantiationStrategy method) instantiation (immuneML.simulation.implants.Motif.Motif attribute) 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) INVALID_P_VALUE (immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper.SequenceFilterHelper attribute) IReceptorImport (class in immuneML.IO.dataset_import.IReceptorImport) 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_repertoire (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) is_simple_type() (immuneML.util.NumpyHelper.NumpyHelper static method) items (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute)

J

JACCARD (immuneML.analysis.similarities.SimilarityMeasureType.SimilarityMeasureType attribute) (immuneML.encodings.distance_encoding.DistanceMetricType.DistanceMetricType attribute)

jaccard() (in module immuneML.util.DistanceMetrics) junction_to_cdr3() (immuneML.util.ImportHelper.ImportHelper static method)

K

K_FOLD (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) k_fold_split() (immuneML.workflows.steps.data_splitter.DataSplitter.DataSplitter static method) KAPPA (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) 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.PreprocessingParser.PreprocessingParser attribute) (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute) (immuneML.dsl.InstructionParser.InstructionParser attribute) KMER_PAIR (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) 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.KNN)

L

L2 (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) Label (class in immuneML.environment.Label) 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) LabelConfiguration (class in immuneML.environment.LabelConfiguration) LabelHelper (class in immuneML.dsl.instruction_parsers.LabelHelper) labels_with_values (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) 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) LIGHT (immuneML.data_model.receptor.receptor_sequence.Chain.Chain attribute) load() (immuneML.dsl.DefaultParamsLoader.DefaultParamsLoader static method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method)

load_attribute() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) load_chains() (immuneML.util.ImportHelper.ImportHelper static method) load_chains_from_chains() (immuneML.util.ImportHelper.ImportHelper static method) load_chains_from_genes() (immuneML.util.ImportHelper.ImportHelper static method) load_data() (immuneML.data_model.repertoire.Repertoire.Repertoire method) load_dataset_if_exists() (immuneML.util.ImportHelper.ImportHelper static method) load_encoded_data() (in module immuneML.dev_util.util) load_encoder() (immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder.AtchleyKmerEncoder static method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder static method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method) (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder static method) (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder static method) (immuneML.encodings.word2vec.Word2VecEncoder.Word2VecEncoder static method) load_repertoire_as_object() (immuneML.util.ImportHelper.ImportHelper static method) load_sequence_dataframe() (immuneML.util.ImportHelper.ImportHelper static method) load_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) log() (in module immuneML.util.Logger) LOG_FILENAME (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) log_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) LOG_LOSS (immuneML.ml_metrics.Metric.Metric attribute) LogisticRegression (class in immuneML.ml_methods.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.api.galaxy.build_dataset_yaml) (in module immuneML.api.galaxy.build_yaml_from_arguments) (in module immuneML.app.ImmuneMLApp) (in module immuneML.workflows.instructions.quickstart) make_binary_class_mapping() (immuneML.ml_methods.util.Util.Util static method) make_class_mapping() (immuneML.ml_methods.util.Util.Util static method) make_data_loader() (immuneML.ml_methods.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_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_gene_columns() (immuneML.IO.dataset_import.SingleLineReceptorImport.SingleLineReceptorImport static method) 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.SimulationHTMLBuilder.SimulationHTMLBuilder static method) (immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder static method) make_ml_methods_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_new_metadata_file() (immuneML.util.ImportHelper.ImportHelper static method) make_preprocessing_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_presentation_builder() (immuneML.presentation.PresentationFactory.PresentationFactory static method) make_report_builder() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) make_reports_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_simulation_docs() (immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser static method) make_subset() (immuneML.data_model.dataset.Dataset.Dataset method) (immuneML.data_model.dataset.ElementDataset.ElementDataset method) (immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset method) (immuneML.data_model.receptor.ElementGenerator.ElementGenerator method) make_trainmlmodel_docs() (immuneML.dsl.InstructionParser.InstructionParser static method) 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_repertoire() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) match_sequence() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) MatchedReceptorsEncoder (class in immuneML.encodings.reference_encoding.MatchedReceptorsEncoder) MatchedReceptorsRepertoireEncoder (class in immuneML.encodings.reference_encoding.MatchedReceptorsRepertoireEncoder) 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) MatchedSequencesRepertoireEncoder (class in immuneML.encodings.reference_encoding.MatchedSequencesRepertoireEncoder) 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_overlap_sliding() (immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery method) max_sequence_length (immuneML.environment.EnvironmentSettings.EnvironmentSettings 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_tmp_batches_to_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) metadata_column_mapping (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) metadata_file (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) MetadataRepertoireFilter (class in immuneML.preprocessing.filters.MetadataRepertoireFilter) method (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) Metric (class in immuneML.ml_metrics.Metric) metrics (immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState attribute) MIN (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) min_count (immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig attribute) min_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) MiXCRImport (class in immuneML.IO.dataset_import.MiXCRImport) ml_details_path (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) 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) 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.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) MLSubseqPerformance (class in immuneML.reports.train_ml_model_reports.MLSubseqPerformance) model (immuneML.encodings.EncoderParams.EncoderParams 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.RepertoireSimilarityComputer 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.build_dataset_yaml immuneML.api.galaxy.build_yaml_from_arguments 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.data_model.cell immuneML.data_model.cell.Cell immuneML.data_model.cell.CellList immuneML.data_model.dataset immuneML.data_model.dataset.Dataset immuneML.data_model.dataset.ElementDataset immuneML.data_model.dataset.ReceptorDataset immuneML.data_model.dataset.RepertoireDataset immuneML.data_model.dataset.SequenceDataset immuneML.data_model.DatasetItem immuneML.data_model.encoded_data immuneML.data_model.encoded_data.EncodedData immuneML.data_model.receptor immuneML.data_model.receptor.BCKReceptor immuneML.data_model.receptor.BCReceptor immuneML.data_model.receptor.ChainPair immuneML.data_model.receptor.ElementGenerator immuneML.data_model.receptor.Receptor immuneML.data_model.receptor.receptor_sequence immuneML.data_model.receptor.receptor_sequence.Chain immuneML.data_model.receptor.receptor_sequence.ReceptorSequence immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation immuneML.data_model.receptor.receptor_sequence.SequenceFrameType immuneML.data_model.receptor.receptor_sequence.SequenceMetadata immuneML.data_model.receptor.ReceptorBuilder immuneML.data_model.receptor.RegionType immuneML.data_model.receptor.TCABReceptor immuneML.data_model.receptor.TCGDReceptor immuneML.data_model.repertoire immuneML.data_model.repertoire.Repertoire 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.SimulationParser 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.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.filtered_sequence_encoding immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper 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.MatchedReceptorsRepertoireEncoder immuneML.encodings.reference_encoding.MatchedReferenceUtil immuneML.encodings.reference_encoding.MatchedRegexEncoder immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder immuneML.encodings.reference_encoding.MatchedSequencesEncoder immuneML.encodings.reference_encoding.MatchedSequencesRepertoireEncoder 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.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_export.ImmuneMLExporter 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.ImmuneMLImport 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.SingleLineReceptorImport 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.AtchleyKmerMILClassifier immuneML.ml_methods.DeepRC immuneML.ml_methods.KNN immuneML.ml_methods.LogisticRegression immuneML.ml_methods.MLMethod immuneML.ml_methods.PrecomputedKNN immuneML.ml_methods.ProbabilisticBinaryClassifier immuneML.ml_methods.pytorch_implementations immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN immuneML.ml_methods.RandomForestClassifier immuneML.ml_methods.ReceptorCNN immuneML.ml_methods.SklearnMethod immuneML.ml_methods.SVC immuneML.ml_methods.SVM immuneML.ml_methods.TCRdistClassifier immuneML.ml_methods.util immuneML.ml_methods.util.Util immuneML.ml_metrics immuneML.ml_metrics.Metric 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.Preprocessor 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.SimulationHTMLBuilder 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.CytoscapeNetworkExporter immuneML.reports.data_reports.DataReport immuneML.reports.data_reports.GLIPH2Exporter immuneML.reports.data_reports.ReceptorDatasetOverview immuneML.reports.data_reports.SequenceLengthDistribution 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.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.MLSubseqPerformance 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.Implanting 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.motif_instantiation_strategy.GappedKmerInstantiation immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy immuneML.simulation.sequence_implanting immuneML.simulation.sequence_implanting.GappedMotifImplanting immuneML.simulation.sequence_implanting.SequenceImplantingStrategy immuneML.simulation.signal_implanting_strategy immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting immuneML.simulation.signal_implanting_strategy.ImplantingComputation immuneML.simulation.signal_implanting_strategy.ReceptorImplanting immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy immuneML.simulation.Simulation immuneML.simulation.SimulationState 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.ReflectionHandler immuneML.util.RepertoireBuilder immuneML.util.SequenceAnalysisHelper 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.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.SimulationInstruction immuneML.workflows.instructions.subsampling immuneML.workflows.instructions.subsampling.SubsamplingInstruction immuneML.workflows.instructions.subsampling.SubsamplingState 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.SignalImplanter 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) MotifInstantiationStrategy (class in immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy) MotifParser (class in immuneML.dsl.definition_parsers.MotifParser) 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.simulation.SimulationState.SimulationState attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) name_chain1 (immuneML.simulation.implants.Motif.Motif attribute) name_chain2 (immuneML.simulation.implants.Motif.Motif attribute) NameBuilder (class in immuneML.util.NameBuilder) 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) 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) OUT (immuneML.data_model.receptor.receptor_sequence.SequenceFrameType.SequenceFrameType attribute) OUTPUT (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) output_figures (immuneML.reports.ReportResult.ReportResult attribute) OUTPUT_FILENAME (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) output_filename (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

paired (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams 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.PreprocessingParser.PreprocessingParser 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) 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(immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) PositionHelper (class in immuneML.util.PositionHelper) PRECISION (immuneML.ml_metrics.Metric.Metric attribute)

PrecomputedKNN (class in immuneML.ml_methods.PrecomputedKNN) predict() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) predict_proba() (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) predictions_path (immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState attribute) prepare_caching_params() 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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.MiXCRImport.MiXCRImport 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.util.AdaptiveImportHelper.AdaptiveImportHelper static method) preprocess_dataset() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) PREPROCESSED (immuneML.data_model.dataset.Dataset.Dataset attribute) 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_performances() (immuneML.workflows.instructions.TrainMLModelInstruction.TrainMLModelInstruction method) ProbabilisticBinaryClassifier (class in 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(immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) PRODUCTION (immuneML.caching.CacheType.CacheType attribute) PyTorchLogisticRegression (class in immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression) PyTorchReceptorCNN (class in immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN)

Q

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

R

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S

safe_load_dataframe() (immuneML.util.ImportHelper.ImportHelper static method) scale_normalized() (immuneML.encodings.kmer_frequency.KmerFrequencyEncoder.KmerFrequencyEncoder method) seed (immuneML.simulation.implants.Motif.Motif attribute) seed_chain1 (immuneML.simulation.implants.Motif.Motif attribute) seed_chain2 (immuneML.simulation.implants.Motif.Motif attribute) 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) SEQUENCE (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) SEQUENCE_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) sequence_file_size (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) SEQUENCE_NAME_MAP (immuneML.IO.dataset_import.MiXCRImport.MiXCRImport attribute) sequence_type (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) SequenceAbundanceEncoder (class in immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder) SequenceAnalysisHelper (class in immuneML.util.SequenceAnalysisHelper) SequenceAnnotation (class in immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation) SequenceAssociationLikelihood (class in immuneML.reports.ml_reports.SequenceAssociationLikelihood) SequenceDataset (class in immuneML.data_model.dataset.SequenceDataset) SequenceEncodingStrategy (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy) SequenceEncodingType (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType) SequenceFilterHelper (class in immuneML.encodings.filtered_sequence_encoding.SequenceFilterHelper) SequenceFrameType (class in immuneML.data_model.receptor.receptor_sequence.SequenceFrameType) SequenceImplantingStrategy (class in immuneML.simulation.sequence_implanting.SequenceImplantingStrategy) SequenceLengthDistribution (class in immuneML.reports.data_reports.SequenceLengthDistribution) SequenceMatcher (class in immuneML.analysis.SequenceMatcher) SequenceMatchingSummaryType (class in immuneML.encodings.reference_encoding.SequenceMatchingSummaryType) SequenceMetadata (class in immuneML.data_model.receptor.receptor_sequence.SequenceMetadata) SequenceModelCreator (class in immuneML.encodings.word2vec.model_creator.SequenceModelCreator) sequences (immuneML.data_model.repertoire.Repertoire.Repertoire property) SequenceType (class in immuneML.environment.SequenceType) set_annotation() (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence method) set_cache() (immuneML.app.ImmuneMLApp.ImmuneMLApp method) set_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings 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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_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 (immuneML.data_model.receptor.receptor_sequence.SequenceFrameType.SequenceFrameType attribute) STOP_CODON (immuneML.environment.Constants.Constants attribute) store() (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.onehot.OneHotEncoder.OneHotEncoder method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.ml_methods.AtchleyKmerMILClassifier.AtchleyKmerMILClassifier method) (immuneML.ml_methods.DeepRC.DeepRC method) (immuneML.ml_methods.MLMethod.MLMethod method) (immuneML.ml_methods.ProbabilisticBinaryClassifier.ProbabilisticBinaryClassifier method) (immuneML.ml_methods.ReceptorCNN.ReceptorCNN method) (immuneML.ml_methods.SklearnMethod.SklearnMethod method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) (immuneML.util.EncoderHelper.EncoderHelper static method) (immuneML.workflows.steps.MLMethodTrainer.MLMethodTrainer static method) store_encoder() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) store_sequence_items() (immuneML.util.ImportHelper.ImportHelper static method) store_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) 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) strip_alleles() (immuneML.util.ImportHelper.ImportHelper static method) strip_genes() (immuneML.util.ImportHelper.ImportHelper static method) strip_suffix() (immuneML.util.ImportHelper.ImportHelper static method) SubjectRepertoireCollector (class in immuneML.preprocessing.SubjectRepertoireCollector) SUBSAMPLED (immuneML.data_model.dataset.Dataset.Dataset attribute) 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) SUM (immuneML.analysis.data_manipulation.ReductionMethod.ReductionMethod attribute) (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) SVC (class in immuneML.ml_methods.SVC) SVM (class in immuneML.ml_methods.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

TCABReceptor (class in immuneML.data_model.receptor.TCABReceptor) TCGDReceptor (class in immuneML.data_model.receptor.TCGDReceptor) TCRB_RELATIVE_ABUNDANCE (immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType.RelativeAbundanceType attribute) TCRdistClassifier (class in immuneML.ml_methods.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) (immuneML.data_model.dataset.Dataset.Dataset attribute) test_dataset (immuneML.hyperparameter_optimization.states.HPItem.HPItem 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.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.filtered_sequence_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder attribute) TRA_TRB (immuneML.data_model.receptor.ChainPair.ChainPair attribute) TRAIN (immuneML.data_model.dataset.Dataset.Dataset attribute) train_dataset (immuneML.hyperparameter_optimization.states.HPItem.HPItem 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_method() (immuneML.hyperparameter_optimization.core.HPUtil.HPUtil static method) train_predictions_path (immuneML.hyperparameter_optimization.states.HPItem.HPItem attribute) training_percentage (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) TRG_TRD (immuneML.data_model.receptor.ChainPair.ChainPair attribute)

U

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_gene_columns() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) update_gene_info() (immuneML.util.ImportHelper.ImportHelper static method) update_report_paths() (immuneML.presentation.html.Util.Util static method) update_result_paths() (immuneML.api.galaxy.Util.Util static method)

update_specs() (immuneML.api.galaxy.GalaxyYamlTool.GalaxyYamlTool 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

VALID_KEYS (immuneML.dsl.definition_parsers.SignalParser.SignalParser attribute) valid_keys (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute) VDJdbImport (class in immuneML.IO.dataset_import.VDJdbImport) version (immuneML.data_model.receptor.BCKReceptor.BCKReceptor attribute) (immuneML.data_model.receptor.BCReceptor.BCReceptor attribute) (immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence attribute) (immuneML.data_model.receptor.TCABReceptor.TCABReceptor attribute) (immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor attribute)

VERSION (immuneML.environment.Constants.Constants attribute)

W

W2VRepertoireEncoder (class in immuneML.encodings.word2vec.W2VRepertoireEncoder) Word2VecEncoder (class in immuneML.encodings.word2vec.Word2VecEncoder)

write_repertoire_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) write_sequence_set_file() (immuneML.encodings.filtered_sequence_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method)