Index

_

__init__() (immuneML.reports.data_reports.DataReport.DataReport method) (immuneML.reports.encoding_reports.EncodingReport.EncodingReport method) (immuneML.reports.train_gen_model_reports.KLKmerComparison.KLKmerComparison method) (immuneML.reports.train_gen_model_reports.TrainGenModelReport.TrainGenModelReport method)

A

AbundanceEncoderHelper (class in immuneML.encodings.abundance_encoding.AbundanceEncoderHelper) ACCURACY (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric 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_cdr3_from_junction() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) (immuneML.util.ImportHelper.ImportHelper static method) add_cl_result_per_run() (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState method) add_default_allele_to_v_gene() (immuneML.util.TCRdistHelper.TCRdistHelper static method) add_default_fields_for_airr_seq_set() (immuneML.util.ImportHelper.ImportHelper static method) add_diagonal() (immuneML.reports.encoding_reports.FeatureComparison.FeatureComparison method) add_encoded_data() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) add_items_for_repertoire() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) add_label() (immuneML.environment.LabelConfiguration.LabelConfiguration method) add_neutral_values() (in module immuneML.data_model.bnp_util) add_single_axis_labels() (immuneML.reports.PlotlyUtil.PlotlyUtil static method) AIRRExporter (class in immuneML.IO.dataset_export.AIRRExporter) AIRRImport (class in immuneML.IO.dataset_import.AIRRImport) ALL (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) (immuneML.util.ReadsType.ReadsType attribute) all_direct_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method) all_nonabstract_subclass_basic_names() (immuneML.util.ReflectionHandler.ReflectionHandler static method) all_nonabstract_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method)

all_possible_instances (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) all_subclasses() (immuneML.util.ReflectionHandler.ReflectionHandler static method) ALLELE_DELIMITER (immuneML.environment.Constants.Constants attribute) allow_negative_aas (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams attribute) ALPHA (immuneML.data_model.SequenceParams.Chain attribute) alphabet_size (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.EncodedLookup property) alphabet_weights (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) AMINO_ACID (immuneML.environment.SequenceType.SequenceType attribute) AND (immuneML.analysis.criteria_matches.BooleanType.BooleanType attribute) annotate_sequences() (in module immuneML.simulation.util.util) assert_all_in_valid_list() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_all_type_and_value() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_any_value_present() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_in_valid_list() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_keys() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_keys_present() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_region_type() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_sequence_type() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_type_and_value() (immuneML.util.ParameterValidator.ParameterValidator static method) assert_valid_tabular_file() (immuneML.util.ParameterValidator.ParameterValidator static method) assign_duplicate_counts() (in module immuneML.simulation.util.util) ATCHLEY_FACTOR_COUNT (immuneML.encodings.atchley_kmer_encoding.Util.Util attribute) ATCHLEY_FACTORS (immuneML.encodings.atchley_kmer_encoding.Util.Util attribute) AUC (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) AVG (immuneML.analysis.data_manipulation.ReductionMethod.ReductionMethod attribute)

B

BALANCED_ACCURACY (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) BETA (immuneML.data_model.SequenceParams.Chain attribute) BINARY (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) bnp_dataclass (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) (immuneML.data_model.SequenceSet.Repertoire property) bnp_read_from_file() (in module immuneML.data_model.bnp_util) bnp_write_to_file() (in module immuneML.data_model.bnp_util) BooleanType (class in immuneML.analysis.criteria_matches.BooleanType) buffer_type (immuneML.data_model.datasets.ElementDataset.ElementDataset property) (immuneML.data_model.SequenceSet.Repertoire property) build() (immuneML.data_model.datasets.ElementDataset.ReceptorDataset class method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset class method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset class method) (immuneML.data_model.SequenceSet.Repertoire class method) (immuneML.presentation.html.FeasibilitySummaryHTMLBuilder.FeasibilitySummaryHTMLBuilder static method) (immuneML.simulation.implants.LigoPWM.LigoPWM class method) (immuneML.util.PathBuilder.PathBuilder static method) (immuneML.util.RepertoireBuilder.RepertoireBuilder static method) build_abundance_matrix() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) build_comparison_data() (immuneML.util.EncoderHelper.EncoderHelper static method) build_comparison_params() (immuneML.util.EncoderHelper.EncoderHelper static method) build_dataset() (immuneML.util.RepertoireBuilder.RepertoireBuilder static method) build_distance_matrix() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) build_dynamic_airr_sequence_set_dataclass() (in module immuneML.data_model.SequenceSet) build_dynamic_bnp_dataclass() (in module immuneML.data_model.bnp_util) build_dynamic_bnp_dataclass_obj() (in module immuneML.data_model.bnp_util) build_from_dc_object() (immuneML.data_model.SequenceSet.Repertoire class method) build_from_objects() (immuneML.data_model.datasets.Dataset.Dataset class method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset class method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset class method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset class method) build_from_partial_df() (immuneML.data_model.datasets.ElementDataset.SequenceDataset class method) build_from_sequences() (immuneML.data_model.SequenceSet.Repertoire class method) build_imgt_positions() (in module immuneML.simulation.util.util) build_labels() (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) build_like() (immuneML.data_model.SequenceSet.Repertoire class method) build_name_from_dict() (immuneML.util.NameBuilder.NameBuilder static method) build_object() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder 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.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder 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.example_weighting.ExampleWeightingStrategy.ExampleWeightingStrategy static method) (immuneML.example_weighting.predefined_weighting.PredefinedWeighting.PredefinedWeighting static method) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams class method) (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport class method) (immuneML.ml_methods.generative_models.OLGA.OLGA class method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter class method) (immuneML.preprocessing.filters.SequenceLengthFilter.SequenceLengthFilter class method) (immuneML.preprocessing.ReferenceSequenceAnnotator.ReferenceSequenceAnnotator class method) (immuneML.reports.clustering_reports.ClusteringReport.ClusteringReport class method) (immuneML.reports.clustering_reports.ExternalLabelClusterSummary.ExternalLabelClusterSummary class method) (immuneML.reports.clustering_reports.ExternalLabelMetricHeatmap.ExternalLabelMetricHeatmap class method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter class method) (immuneML.reports.data_reports.LabelOverlap.LabelOverlap 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.gen_model_reports.PWMSummary.PWMSummary class method) (immuneML.reports.Report.Report class method) (immuneML.reports.train_gen_model_reports.KLKmerComparison.KLKmerComparison class method)

build_reports() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) build_specs() (in module immuneML.api.galaxy.build_apply_gen_model_specs) (in module immuneML.api.galaxy.build_dummy_data_simulation_yaml) (in module immuneML.api.galaxy.build_ligo_yaml)

C

c_call (immuneML.data_model.SequenceSet.ReceptorSequence attribute) 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) camel_case_to_word_string() (immuneML.util.StringHelper.StringHelper static method) camel_case_to_words() (immuneML.util.StringHelper.StringHelper static method) can_compute_p_gens() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) can_generate_from_skewed_gene_models() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) cell_id (immuneML.data_model.SequenceSet.Receptor attribute) (immuneML.data_model.SequenceSet.ReceptorSequence attribute) Chain (class in immuneML.data_model.SequenceParams) chain_1 (immuneML.data_model.SequenceSet.Receptor attribute) chain_2 (immuneML.data_model.SequenceSet.Receptor attribute) chain_pair (immuneML.data_model.SequenceSet.Receptor attribute) ChainPair (class in immuneML.data_model.SequenceParams) ChainRepertoireFilter (class in immuneML.preprocessing.filters.ChainRepertoireFilter) check() (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) check_clonal_frequency() (in module immuneML.dsl.definition_parsers.SignalParser) check_compairr_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) check_dataset_not_empty() (immuneML.preprocessing.filters.Filter.Filter method) check_dataset_type() (immuneML.preprocessing.Preprocessor.Preprocessor method) check_dataset_type_available_in_mapping() (immuneML.util.EncoderHelper.EncoderHelper static method) check_is_positive_class() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) check_iteration_progress() (in module immuneML.simulation.util.util) check_label_format() (immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper static method) check_positive_class_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) check_prerequisites() (immuneML.reports.clustering_reports.ExternalLabelClusterSummary.ExternalLabelClusterSummary method) (immuneML.reports.clustering_reports.ExternalLabelMetricHeatmap.ExternalLabelMetricHeatmap method) (immuneML.reports.data_reports.GLIPH2Exporter.GLIPH2Exporter method) (immuneML.reports.data_reports.LabelOverlap.LabelOverlap 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.gen_model_reports.PWMSummary.PWMSummary method) (immuneML.reports.Report.Report method) check_sequence_count() (in module immuneML.simulation.util.util) check_sim_strategy_setup() (in module immuneML.dsl.definition_parsers.SimulationParser) choose_implant_position() (in module immuneML.simulation.util.util) cl_setting (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) CLASSIFICATION (immuneML.environment.LabelType.LabelType attribute) ClassificationMetric (class in immuneML.ml_metrics.ClassificationMetric) clonal_frequency (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) CLONAL_PERCENTAGE (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) clone() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ElementDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) ClonesPerRepertoireFilter (class in immuneML.preprocessing.filters.ClonesPerRepertoireFilter) clustering_items (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) clustering_method (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) clustering_method_name (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) clustering_params (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) clustering_report_results (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) clustering_settings (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) ClusteringConfig (class in immuneML.workflows.instructions.clustering.ClusteringState) ClusteringItem (class in immuneML.workflows.instructions.clustering.clustering_run_model) ClusteringItemResult (class in immuneML.workflows.instructions.clustering.ClusteringState) ClusteringMethod (class in immuneML.ml_methods.clustering.ClusteringMethod) ClusteringMethodReport (class in immuneML.reports.clustering_method_reports.ClusteringMethodReport) ClusteringReport (class in immuneML.reports.clustering_reports.ClusteringReport) ClusteringReportHandler (class in immuneML.workflows.instructions.clustering.ClusteringReportHandler)

ClusteringResultPerRun (class in immuneML.workflows.instructions.clustering.ClusteringState) ClusteringResults (class in immuneML.workflows.instructions.clustering.ClusteringState) ClusteringSetting (class in immuneML.workflows.instructions.clustering.clustering_run_model) ClusteringState (class in immuneML.workflows.instructions.clustering.ClusteringState) 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) column_mapping (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) column_mapping_synonyms (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) columns_to_load (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) COMMENT_SIGN (immuneML.environment.Constants.Constants attribute) compairr_path (immuneML.util.CompAIRRParams.CompAIRRParams attribute) compairr_paths (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) CompAIRRBatchIterator (class in immuneML.encodings.abundance_encoding.CompAIRRBatchIterator) CompAIRRDistanceEncoder (class in immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder) CompAIRRHelper (class in immuneML.util.CompAIRRHelper) CompAIRRParams (class in immuneML.util.CompAIRRParams) CompAIRRSequenceAbundanceEncoder (class in immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder) compare() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) compare_repertoires() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) ComparisonData (class in immuneML.pairwise_repertoire_comparison.ComparisonData) ComparisonDataBatch (class in immuneML.pairwise_repertoire_comparison.ComparisonDataBatch) compute_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_p_gen() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) compute_p_gens() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) compute_relative_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_sequence_count() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) compute_tcr_dist() (immuneML.util.TCRdistHelper.TCRdistHelper static method) compute_tcrb_relative_abundance() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) compute_weights() (immuneML.example_weighting.ExampleWeightingStrategy.ExampleWeightingStrategy method) (immuneML.example_weighting.predefined_weighting.PredefinedWeighting.PredefinedWeighting method) config (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) CONFUSION_MATRIX (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) Constants (class in immuneML.environment.Constants) construct_sequence_metadata_object() (in module immuneML.simulation.util.util) contains() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) CONTINUOUS_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) convert_enums_to_str() (in module immuneML.data_model.bnp_util) convert_to_expected_types() (in module immuneML.data_model.bnp_util) convert_to_snake_case() (immuneML.dsl.DefaultParamsLoader.DefaultParamsLoader static method) CORES (immuneML.analysis.SequenceMatcher.SequenceMatcher attribute) COUNT (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) count_threshold (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams 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_comparison_data() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) create_gapped_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_gapped_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_gapped_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_IMGT_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_from_sequence() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_from_string() (immuneML.util.KmerHelper.KmerHelper static method) create_kmers_within_HD() (immuneML.util.KmerHelper.KmerHelper static method) create_label_config() (immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper static method) create_metadata_dict() (immuneML.data_model.datasets.Dataset.Dataset class method) (immuneML.data_model.datasets.ElementDataset.ElementDataset class method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset class 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_sentences_from_repertoire() (immuneML.util.KmerHelper.KmerHelper static method) CriteriaMatcher (class in immuneML.analysis.criteria_matches.CriteriaMatcher) CriteriaTypeInstantiator (class in immuneML.analysis.criteria_matches.CriteriaTypeInstantiator) CSS_PATH (immuneML.presentation.html.FeasibilitySummaryHTMLBuilder.FeasibilitySummaryHTMLBuilder attribute) custom_func_keys (immuneML.dsl.definition_parsers.SignalParser.SignalParser attribute) CUTOFF (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute)

D

d_call (immuneML.data_model.SequenceSet.ReceptorSequence attribute) data (immuneML.data_model.datasets.ElementDataset.ElementDataset property) (immuneML.data_model.SequenceSet.Repertoire property) data_filename (immuneML.data_model.SequenceSet.Repertoire attribute) DataEncoder (class in immuneML.workflows.steps.DataEncoder) DataEncoderParams (class in immuneML.workflows.steps.DataEncoderParams) DataExporter (class in immuneML.IO.dataset_export.DataExporter) DataFrameWrapper (class in immuneML.workflows.instructions.clustering.clustering_run_model) 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.datasets.Dataset) DATASET (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) dataset (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) (immuneML.workflows.steps.DataEncoderParams.DataEncoderParams attribute) (immuneML.workflows.steps.DataWeighterParams.DataWeighterParams attribute) dataset_file (immuneML.data_model.datasets.Dataset.Dataset attribute) (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) DATASET_FORMAT (immuneML.util.ImportHelper.ImportHelper attribute) dataset_mapping (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) (immuneML.encodings.onehot.OneHotEncoder.OneHotEncoder attribute) (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder attribute) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder attribute) DatasetEncoder (class in immuneML.encodings.DatasetEncoder) 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) DatasetImportParams (class in immuneML.IO.dataset_import.DatasetImportParams) datasets (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) DataSplitterParams (class in immuneML.workflows.steps.data_splitter.DataSplitterParams) DataWeighter (class in immuneML.workflows.steps.DataWeighter) DataWeighterParams (class in immuneML.workflows.steps.DataWeighterParams) decode() (immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator.SimpleVAEGenerator method) Decoder (class in immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator) DeepRCEncoder (class in immuneML.encodings.deeprc.DeepRCEncoder)

default_analysis_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) default_clonal_frequency (immuneML.simulation.SimConfigItem.SimConfigItem attribute) DEFAULT_MODEL_FOLDER_MAP (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) default_model_name (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) default_params_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) DefaultParamsLoader (class in immuneML.dsl.DefaultParamsLoader) DefinitionParserOutput (class in immuneML.dsl.definition_parsers.DefinitionParserOutput) DELTA (immuneML.data_model.SequenceParams.Chain attribute) DesignMatrixExporter (class in immuneML.reports.encoding_reports.DesignMatrixExporter) determine_compairr_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) determine_repertoire_dataset_labels() (immuneML.IO.dataset_import.DataImport.DataImport method) determine_repertoire_type_dict() (immuneML.IO.dataset_import.DataImport.DataImport method) differences (immuneML.util.CompAIRRParams.CompAIRRParams attribute) dim_red_name (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) dim_red_params (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) dim_reduction (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) dim_reduction_method (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) DimRedMethod (class in immuneML.ml_methods.dim_reduction.DimRedMethod) discover_classes_by_partial_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) discovery (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResults attribute) discovery_datasets (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) DistanceEncoder (class in immuneML.encodings.distance_encoding.DistanceEncoder) DistanceMetricType (class in immuneML.encodings.distance_encoding.DistanceMetricType) do_repertoire_overlap (immuneML.util.CompAIRRParams.CompAIRRParams attribute) do_sequence_matching (immuneML.util.CompAIRRParams.CompAIRRParams attribute) DocEnumHelper (class in immuneML.util.DocEnumHelper) DOCS_TITLE (immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod attribute) (immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod attribute) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel attribute) (immuneML.reports.clustering_method_reports.ClusteringMethodReport.ClusteringMethodReport attribute) (immuneML.reports.clustering_reports.ClusteringReport.ClusteringReport attribute) (immuneML.reports.data_reports.DataReport.DataReport attribute) (immuneML.reports.encoding_reports.EncodingReport.EncodingReport attribute) (immuneML.reports.gen_model_reports.GenModelReport.GenModelReport attribute) drop_empty_sequences() (immuneML.util.ImportHelper.ImportHelper static method) drop_illegal_character_sequences() (immuneML.util.ImportHelper.ImportHelper static method) duplicate_count (immuneML.data_model.SequenceSet.ReceptorSequence attribute) DuplicateSequenceFilter (class in immuneML.preprocessing.filters.DuplicateSequenceFilter) dynamic_fields (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) (immuneML.data_model.SequenceSet.Repertoire attribute)

E

element_count (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) (immuneML.data_model.SequenceSet.Repertoire property) element_ids (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) ElementDataset (class in immuneML.data_model.datasets.ElementDataset) EmpiricalLengthDistribution (class in immuneML.ml_methods.generative_models.MultinomialKmerModel) encode() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) (immuneML.encodings.distance_encoding.TCRdistEncoder.TCRdistEncoder method) (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder method) (immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder 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.ml_methods.pytorch_implementations.SimpleVAEGenerator.SimpleVAEGenerator method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) encode_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_element_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_labels (immuneML.encodings.EncoderParams.EncoderParams attribute) encode_repertoire() (immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder.EvennessProfileRepertoireEncoder method) encode_repertoire_dataset_labels() (immuneML.util.EncoderHelper.EncoderHelper static method) encode_sequence() (immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder.GappedKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder.IdentitySequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder.IMGTGappedKmerEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder.IMGTKmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder.KmerSequenceEncoder static method) (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy.SequenceEncodingStrategy static method) (immuneML.encodings.kmer_frequency.sequence_encoding.VGeneContKmerEncoder.VGeneContKmerEncoder static method) encoded_data (immuneML.data_model.datasets.Dataset.Dataset attribute) EncodedData (class in immuneML.data_model.EncodedData) EncodedLookup (class in immuneML.ml_methods.generative_models.SequenceTransitionDistribution) Encoder (class in immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator) encoder (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.steps.DataEncoderParams.DataEncoderParams attribute) encoder_name (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) encoder_params (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) (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 (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.EncodedLookup property) encoding_class (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) encoding_file (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) encoding_func() (immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator.SimpleVAEGenerator method) 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) EncodingParser (class in immuneML.dsl.definition_parsers.EncodingParser) EncodingReport (class in immuneML.reports.encoding_reports.EncodingReport) end_probs (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution attribute) EntropyCalculator (class in immuneML.analysis.entropy_calculations.EntropyCalculator) EnvironmentSettings (class in immuneML.environment.EnvironmentSettings) estimate_kmer_model() (in module immuneML.ml_methods.generative_models.MultinomialKmerModel) estimate_length_distribution() (in module immuneML.ml_methods.generative_models.MultinomialKmerModel) estimate_smoothed_length_distribution() (in module immuneML.ml_methods.generative_models.MultinomialKmerModel) estimate_transition_model() (in module immuneML.ml_methods.generative_models.SequenceTransitionDistribution) 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_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_similarities() (in module immuneML.ml_methods.generative_models.KLEvaluator) evaluate_top_n() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) EvennessProfileEncoder (class in immuneML.encodings.evenness_profile.EvennessProfileEncoder) EvennessProfileRepertoireEncoder (class in immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder) example_weighting (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) ExampleWeightingParams (class in immuneML.example_weighting.ExampleWeightingParams) ExampleWeightingParser (class in immuneML.dsl.definition_parsers.ExampleWeightingParser) ExampleWeightingStrategy (class in immuneML.example_weighting.ExampleWeightingStrategy) exists() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.util.ReflectionHandler.ReflectionHandler static method) ExperimentalImport (class in immuneML.ml_methods.generative_models.ExperimentalImport) exploratory_analysis_units (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) ExploratoryAnalysisInstruction (class in immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction) 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) export_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_dataset() (immuneML.util.ExporterHelper.ExporterHelper static method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) export_metadata_file() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) export_pairwise_comparison() (immuneML.IO.ml_method.UtilIO.UtilIO static method) export_repertoire_tsv_files() (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) ExporterHelper (class in immuneML.util.ExporterHelper) extend_dataclass_with_dynamic_fields() (in module immuneML.data_model.bnp_util) EXTENSION (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) external_performance (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) ExternalLabelClusterSummary (class in immuneML.reports.clustering_reports.ExternalLabelClusterSummary) ExternalLabelMetricHeatmap (class in immuneML.reports.clustering_reports.ExternalLabelMetricHeatmap) extract_dict_columns() (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport method) extract_locus_from_data() (immuneML.util.ImportHelper.ImportHelper static method) extract_sequence_dataset_params() (immuneML.util.ImportHelper.ImportHelper static method)

F

F1_MACRO (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) F1_MICRO (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) F1_WEIGHTED (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) false_negative_prob_in_receptors (immuneML.simulation.SimConfigItem.SimConfigItem attribute) false_positive_prob_in_receptors (immuneML.simulation.SimConfigItem.SimConfigItem attribute) FeasibilitySummaryHTMLBuilder (class in immuneML.presentation.html.FeasibilitySummaryHTMLBuilder) FeasibilitySummaryInstruction (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FeasibilitySummaryState (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FeasibilitySumReports (class in immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction) FEATURE_DELIMITER (immuneML.environment.Constants.Constants attribute) FeatureComparison (class in immuneML.reports.encoding_reports.FeatureComparison) FeatureDistribution (class in immuneML.reports.encoding_reports.FeatureDistribution) FeatureReport (class in immuneML.reports.encoding_reports.FeatureReport) FeatureValueBarplot (class in immuneML.reports.encoding_reports.FeatureValueBarplot) file_path (immuneML.simulation.implants.LigoPWM.LigoPWM attribute) filename (immuneML.data_model.datasets.ElementDataset.ElementDataset attribute) FilenameHandler (class in immuneML.util.FilenameHandler) fill_in_neutral_vals() (in module immuneML.data_model.datasets.ElementDataset) Filter (class in immuneML.preprocessing.filters.Filter) filter_existing_items() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) filter_illegal_receptors() (immuneML.util.ImportHelper.ImportHelper static method) filter_illegal_sequences() (immuneML.util.ImportHelper.ImportHelper class method)

filter_out_illegal_sequences() (in module immuneML.simulation.util.util) filter_sequences_by_length() (in module immuneML.simulation.util.util) FIRST (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) fit() (immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod method) (immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) fit_predict() (immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod method) fit_transform() (immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod method) fix_empty_strings_in_metadata() (in module immuneML.data_model.datasets.ElementDataset) formats (immuneML.simulation.LigoSimState.LigoSimState 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) (immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator.SimpleLSTMGenerator method) (immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator.Decoder method) (immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator.Encoder method) (immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator.SimpleVAEGenerator method) from_probabilities() (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution class method) FULL_SEQUENCE (immuneML.data_model.SequenceParams.RegionType attribute)

G

GAMMA (immuneML.data_model.SequenceParams.Chain attribute) GAP_LETTER (immuneML.environment.Constants.Constants attribute) GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) GappedKmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder) gen_imgt_positions_from_cdr3_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_junction_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_length() (immuneML.util.PositionHelper.PositionHelper static method) gen_imgt_positions_from_sequence() (immuneML.util.PositionHelper.PositionHelper static method) GENE_DELIMITER (immuneML.environment.Constants.Constants attribute) generate_cache_key() (immuneML.caching.CacheHandler.CacheHandler static method) generate_from_skewed_gene_models() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) generate_receptor_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_repertoire_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_report() (immuneML.reports.Report.Report method) generate_sequence_dataset() (immuneML.simulation.dataset_generation.RandomDatasetGenerator.RandomDatasetGenerator static method) generate_sequences() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) generative_model (immuneML.simulation.SimConfigItem.SimConfigItem attribute) GenerativeModel (class in immuneML.ml_methods.generative_models.GenerativeModel) GenericImport (class in immuneML.IO.dataset_import.GenericImport) GenModelReport (class in immuneML.reports.gen_model_reports.GenModelReport) genomic_data (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) get() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_additional_files() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) get_all_motif_instances() (immuneML.simulation.implants.Signal.Signal method) get_all_params() (immuneML.dsl.ObjectParser.ObjectParser static method) get_all_possible_instances() (immuneML.simulation.implants.LigoPWM.LigoPWM method) (immuneML.simulation.implants.Motif.Motif method) (immuneML.simulation.implants.SeedMotif.SeedMotif method) get_allowed_positions() (in module immuneML.simulation.util.util) get_allowed_positions_for_annotation() (immuneML.util.PositionHelper.PositionHelper static method) get_alphabet() (immuneML.simulation.implants.LigoPWM.LigoPWM method) (immuneML.simulation.implants.Motif.Motif method) (immuneML.simulation.implants.SeedMotif.SeedMotif method) get_amino_acid_color_map() (immuneML.reports.PlotlyUtil.PlotlyUtil static method) get_atchely_factors() (immuneML.encodings.atchley_kmer_encoding.Util.Util static method) get_attribute() (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.SequenceSet.ReceptorSequence method) get_auxiliary_labels() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_batch_dict() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_batch_from_path() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_batches() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_binary_negative_class() (immuneML.environment.Label.Label method) get_bnp_data() (in module immuneML.simulation.util.util) get_by_key() (immuneML.caching.CacheHandler.CacheHandler static method) get_by_type() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_cache_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_chain() (immuneML.data_model.SequenceParams.Chain static method) get_chain_pair() (immuneML.data_model.SequenceParams.ChainPair static method) get_chain_value() (immuneML.data_model.SequenceParams.Chain static method) get_chains() (immuneML.util.TCRdistHelper.TCRdistHelper static method) get_cl_item() (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun method) get_class() (immuneML.dsl.ObjectParser.ObjectParser static method) get_class_by_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_class_from_path() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_class_name() (immuneML.dsl.ObjectParser.ObjectParser static method) get_classes_by_partial_name() (immuneML.util.ReflectionHandler.ReflectionHandler static method) get_cmd_args() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) get_config() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_css_content() (immuneML.presentation.html.Util.Util static method) get_current_dataset() (immuneML.util.EncoderHelper.EncoderHelper static method) get_data() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_data_for_clustering() (in module immuneML.ml_methods.clustering.ClusteringMethod) get_data_from_index_range() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_dataset_name() (immuneML.util.FilenameHandler.FilenameHandler static method) get_dataset_simulation_specs() (in module immuneML.api.galaxy.build_dummy_data_simulation_yaml) get_desc_for_storage() (immuneML.environment.Label.Label method) get_df() (immuneML.workflows.instructions.clustering.clustering_run_model.DataFrameWrapper method) get_dimension_names() (immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod method) get_documentation() (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method) (immuneML.encodings.reference_encoding.MatchedRegexEncoder.MatchedRegexEncoder 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.TenxGenomicsImport.TenxGenomicsImport static method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter static method) (immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction.DatasetExportInstruction static method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction static method) get_element_count() (immuneML.data_model.SequenceSet.Repertoire method) get_encoded_repertoire() (immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder.EvennessProfileRepertoireEncoder 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.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_example_ids() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_example_weights_by_identifiers() (immuneML.util.EncoderHelper.EncoderHelper static method) get_examples_as_np_matrix() (immuneML.data_model.EncodedData.EncodedData 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.encodings.kmer_frequency.sequence_encoding.VGeneContKmerEncoder.VGeneContKmerEncoder static method) get_field_type_from_values() (in module immuneML.data_model.bnp_util) get_file_path() (immuneML.caching.CacheHandler.CacheHandler static method) get_filename() (immuneML.util.FilenameHandler.FilenameHandler static method) get_filenames() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_full_specs_path() (immuneML.presentation.html.Util.Util static method) get_imgt_position_weights_for_annotation() (immuneML.util.PositionHelper.PositionHelper static method) get_imgt_position_weights_for_implanting() (immuneML.util.PositionHelper.PositionHelper static method) get_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_key() (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting method) get_keys_by_type() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_kl_weights() (in module immuneML.ml_methods.generative_models.KLEvaluator) get_label_count() (immuneML.environment.LabelConfiguration.LabelConfiguration method) get_label_names() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ElementDataset method) (immuneML.data_model.datasets.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_logfile_path() (immuneML.presentation.html.Util.Util static method) get_matching_func_for_repertoire() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) get_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) get_max_information_gain() (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method) get_max_length() (immuneML.simulation.implants.LigoPWM.LigoPWM method) (immuneML.simulation.implants.Motif.Motif method) (immuneML.simulation.implants.SeedMotif.SeedMotif method) get_max_seq_length() (in module immuneML.simulation.util.util) get_metadata() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_metadata_fields() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_metric() (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric static method) get_min_seq_length() (in module immuneML.simulation.util.util) get_model_name() (immuneML.util.FilenameHandler.FilenameHandler static method) get_no_signal_sequences() (in module immuneML.simulation.util.util) get_numpy_representation() (immuneML.util.NumpyHelper.NumpyHelper static method) get_object() (immuneML.data_model.SequenceParams.RegionType class method) get_params() (immuneML.dsl.ObjectParser.ObjectParser static method) get_plot() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) get_probability_based_metric_types() (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric static method) get_receptor_filter_sort_kwargs() (immuneML.util.ImportHelper.ImportHelper static method) get_receptor_params() (immuneML.encodings.reference_encoding.MatchedReceptorsEncoder.MatchedReceptorsEncoder method) get_region_type() (in module immuneML.simulation.util.util) get_relevant_sequence_attributes() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_relevant_sequence_indices() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) get_repertoire() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_repertoire_contents() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) get_repertoire_filename_from_metadata_row() (immuneML.util.ImportHelper.ImportHelper static method) get_repertoire_ids() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) get_repertoire_vector() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_repertoire_vectors() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_row_by_index() (in module immuneML.data_model.bnp_util) get_rows_by_indices() (in module immuneML.data_model.bnp_util) get_search_criterion() (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric static method) get_seq_name_for_seq_object() (immuneML.encodings.EncoderParams.EncoderParams method) get_sequence() (immuneML.data_model.SequenceSet.ReceptorSequence method) get_sequence_alphabet() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_sequence_field_name() (immuneML.encodings.EncoderParams.EncoderParams method) (in module immuneML.data_model.bnp_util) get_sequence_filenames() (immuneML.util.ImportHelper.ImportHelper static method) get_sequence_identifiers() (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport static method) get_sequence_matching_feature() (immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder method) get_sequence_matching_feature_with_compairr() (immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder method) get_sequence_matching_feature_without_compairr() (immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder method) get_sequence_per_signal_count() (in module immuneML.simulation.util.util) get_sequence_set() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) get_sequence_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) get_sequence_value() (in module immuneML.data_model.SequenceSet) get_sequence_vectors() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) get_signal_sequence_count() (in module immuneML.simulation.util.util) get_signal_sequences() (in module immuneML.simulation.util.util) get_signals() (immuneML.dsl.symbol_table.SymbolTable.SymbolTable method) get_single_label_name_from_config() (immuneML.util.EncoderHelper.EncoderHelper static method) get_single_row_value() (in module immuneML.data_model.bnp_util) get_sklearn_score_name() (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric static method) get_standardized_name() (immuneML.util.ImportHelper.ImportHelper static method) get_subject_ids() (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset 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.ml_methods.dim_reduction.DimRedMethod.DimRedMethod class method) (immuneML.reports.train_gen_model_reports.KLKmerComparison.KLKmerComparison static method) (immuneML.reports.train_gen_model_reports.TrainGenModelReport.TrainGenModelReport static method) get_tmp_batches() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) get_total_seq_count() (immuneML.simulation.SimConfig.SimConfig method) get_total_seq_count_for_signal() (immuneML.simulation.SimConfig.SimConfig method) get_type_dict_from_bnp_object() (in module immuneML.data_model.bnp_util) get_worst_simulated_sequences() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) get_worst_true_sequences() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) GLIPH2Exporter (class in immuneML.reports.data_reports.GLIPH2Exporter) GREATER_THAN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) group_structured_array_by() (immuneML.util.NumpyHelper.NumpyHelper static method)

H

hamming_distance_probabilities (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) hash() (immuneML.caching.CacheHandler.CacheHandler static method) HEAVY (immuneML.data_model.SequenceParams.Chain attribute)

HPAssessmentState (class in immuneML.hyperparameter_optimization.states.HPAssessmentState) HPLabelState (class in immuneML.hyperparameter_optimization.states.HPLabelState) HTML (immuneML.presentation.PresentationFormat.PresentationFormat attribute) html_templates_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute)

I

id (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) ID_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) identifier (immuneML.data_model.datasets.Dataset.Dataset attribute) (immuneML.data_model.SequenceSet.Repertoire attribute) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) (immuneML.simulation.implants.Motif.Motif attribute) (immuneML.simulation.SimConfig.SimConfig 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.SequenceParams.ChainPair attribute) IGH_IGL (immuneML.data_model.SequenceParams.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.SequenceParams.RegionType attribute) IMGT_CDR2 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_CDR3 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_CONTINUOUS_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGT_FR1 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_FR2 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_FR3 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_FR4 (immuneML.data_model.SequenceParams.RegionType attribute) IMGT_GAPPED_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) IMGT_JUNCTION (immuneML.data_model.SequenceParams.RegionType attribute) IMGTGappedKmerEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder) IMGTKmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder) immune_events (immuneML.simulation.SimConfigItem.SimConfigItem attribute) immuneML module immuneML.analysis 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.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.api module immuneML.api.aggregated_runs module immuneML.api.galaxy module immuneML.api.galaxy.build_apply_gen_model_specs module immuneML.api.galaxy.build_dummy_data_simulation_yaml module immuneML.api.galaxy.build_ligo_yaml module immuneML.app module immuneML.caching module immuneML.caching.CacheHandler module immuneML.caching.CacheObjectType module immuneML.caching.CacheType module immuneML.data_model module immuneML.data_model.AIRRSequenceSet module immuneML.data_model.bnp_util module immuneML.data_model.datasets module immuneML.data_model.datasets.Dataset module immuneML.data_model.datasets.ElementDataset module immuneML.data_model.datasets.RepertoireDataset module immuneML.data_model.EncodedData module immuneML.data_model.SequenceParams module immuneML.data_model.SequenceSet 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.DefinitionParserOutput module immuneML.dsl.definition_parsers.EncodingParser module immuneML.dsl.definition_parsers.ExampleWeightingParser 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.import_parsers module immuneML.dsl.import_parsers.ImportParser module immuneML.dsl.instruction_parsers module immuneML.dsl.instruction_parsers.DatasetExportParser module immuneML.dsl.instruction_parsers.LabelHelper module immuneML.dsl.instruction_parsers.SubsamplingParser module immuneML.dsl.ObjectParser 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.dsl.Util module immuneML.encodings module immuneML.encodings.abundance_encoding module immuneML.encodings.abundance_encoding.AbundanceEncoderHelper module immuneML.encodings.abundance_encoding.CompAIRRBatchIterator module immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder module immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder module immuneML.encodings.atchley_kmer_encoding module immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType module immuneML.encodings.atchley_kmer_encoding.Util module immuneML.encodings.DatasetEncoder module immuneML.encodings.deeprc module immuneML.encodings.deeprc.DeepRCEncoder module immuneML.encodings.distance_encoding module immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder module immuneML.encodings.distance_encoding.DistanceEncoder module immuneML.encodings.distance_encoding.DistanceMetricType module immuneML.encodings.distance_encoding.TCRdistEncoder module immuneML.encodings.EncoderParams module immuneML.encodings.evenness_profile module immuneML.encodings.evenness_profile.EvennessProfileEncoder module immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder module immuneML.encodings.kmer_frequency module immuneML.encodings.kmer_frequency.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.kmer_frequency.sequence_encoding.VGeneContKmerEncoder module immuneML.encodings.motif_encoding module immuneML.encodings.motif_encoding.PositionalMotifParams module immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder 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.protein_embedding module immuneML.encodings.reference_encoding module immuneML.encodings.reference_encoding.MatchedReceptorsEncoder module immuneML.encodings.reference_encoding.MatchedReferenceUtil module immuneML.encodings.reference_encoding.MatchedRegexEncoder module immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder module immuneML.encodings.reference_encoding.MatchedSequencesEncoder module immuneML.encodings.reference_encoding.SequenceMatchingSummaryType module immuneML.encodings.word2vec module immuneML.encodings.word2vec.model_creator module immuneML.encodings.word2vec.model_creator.KmerPairModelCreator module immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy module immuneML.encodings.word2vec.model_creator.ModelType module immuneML.encodings.word2vec.model_creator.SequenceModelCreator module immuneML.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.example_weighting module immuneML.example_weighting.ExampleWeightingParams module immuneML.example_weighting.ExampleWeightingStrategy module immuneML.example_weighting.predefined_weighting module immuneML.example_weighting.predefined_weighting.PredefinedWeighting module immuneML.hyperparameter_optimization module immuneML.hyperparameter_optimization.config module immuneML.hyperparameter_optimization.config.ClusterValidationType 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.states module immuneML.hyperparameter_optimization.states.HPAssessmentState module immuneML.hyperparameter_optimization.states.HPLabelState module immuneML.hyperparameter_optimization.strategy module immuneML.IO module immuneML.IO.dataset_export module immuneML.IO.dataset_export.AIRRExporter module immuneML.IO.dataset_export.DataExporter module immuneML.IO.dataset_import module immuneML.IO.dataset_import.AIRRImport module immuneML.IO.dataset_import.DataImport module immuneML.IO.dataset_import.DatasetImportParams module immuneML.IO.dataset_import.GenericImport module immuneML.IO.dataset_import.IGoRImport module immuneML.IO.dataset_import.ImmunoSEQRearrangementImport module immuneML.IO.dataset_import.ImmunoSEQSampleImport module immuneML.IO.dataset_import.IReceptorImport module immuneML.IO.dataset_import.MiXCRImport module immuneML.IO.dataset_import.OLGAImport module immuneML.IO.dataset_import.RandomReceptorDatasetImport module immuneML.IO.dataset_import.RandomRepertoireDatasetImport module immuneML.IO.dataset_import.RandomSequenceDatasetImport module immuneML.IO.dataset_import.TenxGenomicsImport module immuneML.IO.dataset_import.VDJdbImport module immuneML.IO.ml_method module immuneML.IO.ml_method.MLMethodConfiguration module immuneML.IO.ml_method.UtilIO module immuneML.ml_methods module immuneML.ml_methods.classifiers module immuneML.ml_methods.clustering module immuneML.ml_methods.clustering.ClusteringMethod module immuneML.ml_methods.dim_reduction module immuneML.ml_methods.dim_reduction.DimRedMethod module immuneML.ml_methods.generative_models module immuneML.ml_methods.generative_models.BackgroundSequences module immuneML.ml_methods.generative_models.ExperimentalImport module immuneML.ml_methods.generative_models.GenerativeModel module immuneML.ml_methods.generative_models.InternalOlgaModel module immuneML.ml_methods.generative_models.KLEvaluator module immuneML.ml_methods.generative_models.MultinomialKmerModel module immuneML.ml_methods.generative_models.OLGA module

immuneML.ml_methods.generative_models.PWM module immuneML.ml_methods.generative_models.SequenceTransitionDistribution module immuneML.ml_methods.generative_models.SimpleLSTM module immuneML.ml_methods.generative_models.SoNNia module immuneML.ml_methods.helper_methods module immuneML.ml_methods.pytorch_implementations module immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator module immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator module immuneML.ml_methods.util module immuneML.ml_methods.util.pytorch_util module immuneML.ml_metrics module immuneML.ml_metrics.ClassificationMetric module immuneML.ml_metrics.ClusteringMetric 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.MetadataFilter module immuneML.preprocessing.filters.SequenceLengthFilter module immuneML.preprocessing.Preprocessor module immuneML.preprocessing.ReferenceSequenceAnnotator module immuneML.preprocessing.SubjectRepertoireCollector module immuneML.presentation module immuneML.presentation.html module immuneML.presentation.html.FeasibilitySummaryHTMLBuilder module immuneML.presentation.html.Util module immuneML.presentation.InstructionPresentation module immuneML.presentation.PresentationFormat module immuneML.presentation.TemplateParser module immuneML.reports module immuneML.reports.clustering_method_reports module immuneML.reports.clustering_method_reports.ClusteringMethodReport module immuneML.reports.clustering_reports module immuneML.reports.clustering_reports.ClusteringReport module immuneML.reports.clustering_reports.ExternalLabelClusterSummary module immuneML.reports.clustering_reports.ExternalLabelMetricHeatmap module immuneML.reports.data_reports module immuneML.reports.data_reports.DataReport module immuneML.reports.data_reports.GLIPH2Exporter module immuneML.reports.data_reports.LabelOverlap 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.gen_model_reports module immuneML.reports.gen_model_reports.GenModelReport module immuneML.reports.gen_model_reports.PWMSummary module immuneML.reports.ml_reports module immuneML.reports.ml_reports.CoefficientPlottingSetting module immuneML.reports.ml_reports.CoefficientPlottingSettingList module immuneML.reports.multi_dataset_reports module immuneML.reports.PlotlyUtil module immuneML.reports.Report module immuneML.reports.ReportOutput module immuneML.reports.ReportResult module immuneML.reports.train_gen_model_reports module immuneML.reports.train_gen_model_reports.KLKmerComparison module immuneML.reports.train_gen_model_reports.TrainGenModelReport module immuneML.reports.train_ml_model_reports module immuneML.simulation module immuneML.simulation.dataset_generation module immuneML.simulation.dataset_generation.RandomDatasetGenerator module immuneML.simulation.implants module immuneML.simulation.implants.ImplantAnnotation module immuneML.simulation.implants.LigoPWM module immuneML.simulation.implants.Motif module immuneML.simulation.implants.MotifInstance module immuneML.simulation.implants.SeedMotif module immuneML.simulation.implants.Signal module immuneML.simulation.LigoSimState module immuneML.simulation.SimConfig module immuneML.simulation.SimConfigItem module immuneML.simulation.simulation_strategy module immuneML.simulation.simulation_strategy.ImplantingStrategy module immuneML.simulation.simulation_strategy.RejectionSamplingStrategy module immuneML.simulation.simulation_strategy.SimulationStrategy module immuneML.simulation.util module immuneML.simulation.util.bnp_util module immuneML.simulation.util.igor_helper module immuneML.simulation.util.util module immuneML.util module immuneML.util.AdaptiveImportHelper module immuneML.util.CompAIRRHelper module immuneML.util.CompAIRRParams module immuneML.util.DistanceMetrics module immuneML.util.DocEnumHelper module immuneML.util.EncoderHelper module immuneML.util.ExporterHelper module immuneML.util.FilenameHandler module immuneML.util.ImportHelper module immuneML.util.KmerHelper module immuneML.util.Logger module immuneML.util.NameBuilder module immuneML.util.NumpyHelper module immuneML.util.ParameterValidator module immuneML.util.PathBuilder module immuneML.util.PositionHelper module immuneML.util.ReadsType module immuneML.util.ReflectionHandler module immuneML.util.RepertoireBuilder module immuneML.util.StringHelper module immuneML.util.TCRdistHelper module immuneML.workflows module immuneML.workflows.instructions module immuneML.workflows.instructions.apply_gen_model module immuneML.workflows.instructions.clustering module immuneML.workflows.instructions.clustering.clustering_run_model module immuneML.workflows.instructions.clustering.ClusteringReportHandler module immuneML.workflows.instructions.clustering.ClusteringState module immuneML.workflows.instructions.dataset_generation module immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction module immuneML.workflows.instructions.dataset_generation.DatasetExportState module immuneML.workflows.instructions.exploratory_analysis module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState module immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit module immuneML.workflows.instructions.Instruction module immuneML.workflows.instructions.ligo_sim_feasibility module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports module immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction module immuneML.workflows.instructions.ligo_simulation module immuneML.workflows.instructions.ligo_simulation.runtime_reports module immuneML.workflows.instructions.ml_model_application module immuneML.workflows.instructions.subsampling module immuneML.workflows.instructions.subsampling.SubsamplingInstruction module immuneML.workflows.instructions.subsampling.SubsamplingState module immuneML.workflows.instructions.train_gen_model module immuneML.workflows.steps module immuneML.workflows.steps.data_splitter 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.DataWeighter module immuneML.workflows.steps.DataWeighterParams module immuneML.workflows.steps.Step module immuneML.workflows.steps.StepParams module ImmunoSEQRearrangementImport (class in immuneML.IO.dataset_import.ImmunoSEQRearrangementImport) ImmunoSEQSampleImport (class in immuneML.IO.dataset_import.ImmunoSEQSampleImport) ImplantAnnotation (class in immuneML.simulation.implants.ImplantAnnotation) implanting_scaling_factor (immuneML.simulation.SimConfig.SimConfig attribute) ImplantingStrategy (class in immuneML.simulation.simulation_strategy.ImplantingStrategy) import_comparison_data() (immuneML.IO.ml_method.UtilIO.UtilIO static method) import_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.RandomReceptorDatasetImport.RandomReceptorDatasetImport method) (immuneML.IO.dataset_import.RandomRepertoireDatasetImport.RandomRepertoireDatasetImport method) (immuneML.IO.dataset_import.RandomSequenceDatasetImport.RandomSequenceDatasetImport method) import_dataset_from_yaml() (immuneML.IO.dataset_import.DataImport.DataImport method) import_element_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) import_empty_aa_sequences (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_empty_nt_sequences (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_function() (immuneML.util.ReflectionHandler.ReflectionHandler static method) import_illegal_characters (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) 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_productive (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_receptor_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) import_repertoire_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport method) import_repertoire_metadata() (immuneML.IO.dataset_import.DataImport.DataImport method) import_sequence_dataset() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport method) import_unknown_productivity (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_unproductive (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) import_with_stop_codon (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) ImportHelper (class in immuneML.util.ImportHelper) ImportParser (class in immuneML.dsl.import_parsers.ImportParser) IN (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) indels (immuneML.util.CompAIRRParams.CompAIRRParams attribute) info (immuneML.reports.ReportResult.ReportResult attribute) init_zero_state() (immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator.SimpleLSTMGenerator method) initial_distribution (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution attribute) INPUT_FILENAME (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) insert() (immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList method) instantiate() (immuneML.analysis.criteria_matches.CriteriaTypeInstantiator.CriteriaTypeInstantiator static method) instantiate_motif() (immuneML.simulation.implants.LigoPWM.LigoPWM method) (immuneML.simulation.implants.Motif.Motif method) (immuneML.simulation.implants.SeedMotif.SeedMotif method) Instruction (class in immuneML.workflows.instructions.Instruction) INSTRUCTION (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) instruction_class (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) instruction_name (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) InstructionPresentation (class in immuneML.presentation.InstructionPresentation) internal_performance (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) InternalOlgaModel (class in immuneML.ml_methods.generative_models.InternalOlgaModel) INVALID_COLNAME_CHARS (immuneML.util.ImportHelper.ImportHelper attribute) INVALID_P_VALUE (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper attribute) IReceptorImport (class in immuneML.IO.dataset_import.IReceptorImport) is_allowed() (immuneML.data_model.SequenceParams.ChainPair static method) is_cdr3 (immuneML.util.CompAIRRParams.CompAIRRParams attribute) is_external() (in module immuneML.ml_metrics.ClusteringMetric) is_illegal_sequence() (immuneML.util.ImportHelper.ImportHelper static method) is_installed() (immuneML.util.ReflectionHandler.ReflectionHandler static method) is_internal() (in module immuneML.ml_metrics.ClusteringMetric) is_nan_or_empty() (immuneML.util.NumpyHelper.NumpyHelper static method) is_noise (immuneML.simulation.SimConfigItem.SimConfigItem attribute) is_present_custom_func (immuneML.simulation.implants.Signal.Signal attribute) is_repertoire (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.simulation.SimConfig.SimConfig attribute) is_same() (immuneML.ml_methods.generative_models.ExperimentalImport.ExperimentalImport method) (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) is_simple_type() (immuneML.util.NumpyHelper.NumpyHelper static method) is_valid_sequence_str() (in module immuneML.util.AdaptiveImportHelper) is_vdj (immuneML.ml_methods.generative_models.OLGA.OLGA property) item (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringItemResult attribute) items (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun attribute)

J

j_call (immuneML.data_model.SequenceSet.ReceptorSequence attribute) (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property)

j_gene_mapping (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) JACCARD (immuneML.encodings.distance_encoding.DistanceMetricType.DistanceMetricType attribute) jaccard() (in module immuneML.util.DistanceMetrics)

K

K_FOLD (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) KAPPA (immuneML.data_model.SequenceParams.Chain attribute) keep_compairr_input (immuneML.util.CompAIRRParams.CompAIRRParams attribute) keep_p_gen_dist (immuneML.simulation.SimConfig.SimConfig 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.MetadataFilter.MetadataFilter method) (immuneML.preprocessing.Preprocessor.Preprocessor method) (immuneML.preprocessing.SubjectRepertoireCollector.SubjectRepertoireCollector method) KEY_MAPPING (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport attribute) keyword (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser attribute) (immuneML.dsl.definition_parsers.ExampleWeightingParser.ExampleWeightingParser attribute) (immuneML.dsl.definition_parsers.MotifParser.MotifParser attribute) (immuneML.dsl.definition_parsers.PreprocessingParser.PreprocessingParser attribute) (immuneML.dsl.definition_parsers.ReportParser.ReportParser attribute) (immuneML.dsl.definition_parsers.SignalParser.SignalParser attribute) (immuneML.dsl.definition_parsers.SimulationParser.SimulationParser attribute) (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute)

KL() (in module immuneML.ml_methods.generative_models.KLEvaluator) KLEvaluator (class in immuneML.ml_methods.generative_models.KLEvaluator) KLKmerComparison (class in immuneML.reports.train_gen_model_reports.KLKmerComparison) KMER_PAIR (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) KmerDistribution (class in immuneML.ml_methods.generative_models.MultinomialKmerModel) KmerHelper (class in immuneML.util.KmerHelper) KmerModel (class in immuneML.ml_methods.generative_models.MultinomialKmerModel) KmerPairModelCreator (class in immuneML.encodings.word2vec.model_creator.KmerPairModelCreator) KmerSequenceEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder)

L

L2 (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) Label (class in immuneML.environment.Label) label_columns (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) label_config (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) label_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) label_positive_class (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) label_values (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) LabelConfiguration (class in immuneML.environment.LabelConfiguration) LabelHelper (class in immuneML.dsl.instruction_parsers.LabelHelper) LabelOverlap (class in immuneML.reports.data_reports.LabelOverlap) labels (immuneML.data_model.datasets.Dataset.Dataset attribute) LabelType (class in immuneML.environment.LabelType) LAST (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) learn_model (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.example_weighting.ExampleWeightingParams.ExampleWeightingParams attribute) LEAVE_ONE_OUT_STRATIFICATION (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) 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.SequenceParams.Chain attribute) LigoPWM (class in immuneML.simulation.implants.LigoPWM) LigoSimState (class in immuneML.simulation.LigoSimState) load() (immuneML.dsl.DefaultParamsLoader.DefaultParamsLoader static method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution class method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) load_alleles() (in module immuneML.IO.dataset_import.MiXCRImport) load_attribute() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) load_encoded_data() (in module immuneML.dev_util.util) load_encoder() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder static method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder static method) (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder static method)

load_file() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.OLGAImport.OLGAImport method) load_internal_model() (immuneML.ml_methods.generative_models.OLGA.OLGA method) load_model() (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel class method) (immuneML.ml_methods.generative_models.OLGA.OLGA class method) (immuneML.ml_methods.generative_models.PWM.PWM class method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM class method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia class method) load_repertoire_object() (immuneML.IO.dataset_import.DataImport.DataImport method) load_repertoires() (immuneML.IO.dataset_import.DataImport.DataImport method) load_sequence_dataframe() (immuneML.IO.dataset_import.DataImport.DataImport method) load_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) load_type_dict() (in module immuneML.data_model.bnp_util) locus (immuneML.data_model.SequenceSet.ReceptorSequence attribute) (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) locus_species (immuneML.data_model.SequenceSet.ReceptorSequence attribute) log() (in module immuneML.util.Logger) log_dataset_info() (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) LOG_FILENAME (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) log_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) LOG_LOSS (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) log_memory_usage() (in module immuneML.util.Logger) log_prob() (immuneML.ml_methods.generative_models.MultinomialKmerModel.EmpiricalLengthDistribution method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.KmerDistribution method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.KmerModel method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.MultinomialKmerModel method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.Poisson method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.SmoothedLengthDistribution method) (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution method) LOOCV (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) low_memory (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute)

M

main() (in module immuneML.api.galaxy.build_apply_gen_model_specs) (in module immuneML.api.galaxy.build_dummy_data_simulation_yaml) (in module immuneML.api.galaxy.build_ligo_yaml) make_airr_seq_set_object_from_sequences() (in module immuneML.data_model.SequenceSet) make_all_fields_dict_from_receptors() (in module immuneML.data_model.datasets.ElementDataset) make_all_fields_dict_from_sequences() (in module immuneML.data_model.datasets.ElementDataset) make_annotated_dataclass() (in module immuneML.simulation.util.util) make_bnp_annotated_sequences() (in module immuneML.simulation.util.util) make_buffer_type_from_dataset_file() (in module immuneML.data_model.bnp_util) make_dataset() (immuneML.workflows.steps.data_splitter.Util.Util static method) make_dataset_html_map() (immuneML.presentation.html.Util.Util static method) make_downloadable_zip() (immuneML.presentation.html.Util.Util static method) make_element_dataset_objects() (in module immuneML.data_model.bnp_util) make_fisher_function() (immuneML.encodings.abundance_encoding.AbundanceEncoderHelper.AbundanceEncoderHelper static method) make_from_report_result() (in module immuneML.presentation.html.FeasibilitySummaryHTMLBuilder) make_full_airr_seq_set_df() (in module immuneML.data_model.bnp_util) make_gene_call_from_gene_and_allele() (in module immuneML.util.AdaptiveImportHelper) make_html_map() (immuneML.presentation.html.FeasibilitySummaryHTMLBuilder.FeasibilitySummaryHTMLBuilder static method) make_motif_instances() (immuneML.simulation.implants.Signal.Signal method) make_new_metadata_file() (immuneML.util.ImportHelper.ImportHelper static method) make_new_model() (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) make_p_gen_histogram_plot() (in module immuneML.workflows.instructions.ligo_simulation.runtime_reports) make_receptors_from_data() (in module immuneML.data_model.SequenceSet) make_repertoire_dataset_subset() (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) make_repertoire_from_sequences() (in module immuneML.simulation.util.util) make_report_builder() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) make_sequence_paths() (in module immuneML.simulation.util.util) make_sequences_from_data() (in module immuneML.data_model.SequenceSet) make_signal_metadata() (in module immuneML.simulation.util.util) make_skewed_model_files() (in module immuneML.simulation.util.igor_helper) make_subset() (immuneML.data_model.datasets.Dataset.Dataset method) (immuneML.data_model.datasets.ElementDataset.ReceptorDataset method) (immuneML.data_model.datasets.ElementDataset.SequenceDataset method) (immuneML.data_model.datasets.RepertoireDataset.RepertoireDataset method) MANUAL (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) ManualSplitConfig (class in immuneML.hyperparameter_optimization.config.ManualSplitConfig) ManualSplitter (class in immuneML.workflows.steps.data_splitter.ManualSplitter) match() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher method) (immuneML.analysis.SequenceMatcher.SequenceMatcher method) match_genes() (in module immuneML.simulation.util.util) match_motif() (in module immuneML.simulation.util.util) match_motif_group() (in module immuneML.simulation.util.util) match_motif_regexes() (in module immuneML.simulation.util.util) match_repertoire() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) match_sequence() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) MatchedReceptorsEncoder (class in immuneML.encodings.reference_encoding.MatchedReceptorsEncoder) MatchedReferenceUtil (class in immuneML.encodings.reference_encoding.MatchedReferenceUtil) MatchedRegexEncoder (class in immuneML.encodings.reference_encoding.MatchedRegexEncoder) MatchedRegexRepertoireEncoder (class in immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder) MatchedSequencesEncoder (class in immuneML.encodings.reference_encoding.MatchedSequencesEncoder) Matches (class in immuneML.reports.encoding_reports.Matches) matches_gene() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) matches_sequence() (immuneML.analysis.SequenceMatcher.SequenceMatcher method) matrix (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) MAX (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) MAX_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) max_gap (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) MAX_MOTIFS_PER_SEQUENCE (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy attribute) max_points_on_plot (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) max_positions (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams attribute) max_sequence_length (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) MAX_SIG_FREQ (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction attribute) MAX_SIGNALS_PER_SEQUENCE (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy attribute) MEAN (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) memo() (immuneML.caching.CacheHandler.CacheHandler static method) memo_by_params() (immuneML.caching.CacheHandler.CacheHandler static method) (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) merge_dataclass_objects() (in module immuneML.data_model.bnp_util) (in module immuneML.simulation.util.bnp_util) merge_tmp_batches_to_matrix() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) metadata (immuneML.data_model.SequenceSet.Receptor attribute) (immuneML.data_model.SequenceSet.ReceptorSequence attribute) (immuneML.data_model.SequenceSet.Repertoire attribute) METADATA_EXTENSION (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) metadata_file (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) metadata_filename (immuneML.data_model.SequenceSet.Repertoire attribute) METADATA_SEP (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) MetadataFilter (class in immuneML.preprocessing.filters.MetadataFilter) method (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) method_based_validation (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResults attribute) metrics (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) MIDPOINT_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) MIN (immuneML.preprocessing.filters.CountAggregationFunction.CountAggregationFunction attribute) MIN_CDR3_LEN (immuneML.util.PositionHelper.PositionHelper attribute) min_count (immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig attribute) min_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) min_gap (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) min_positions (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams attribute) MIN_RANGE_PROBABILITY (immuneML.simulation.simulation_strategy.ImplantingStrategy.ImplantingStrategy attribute) MIN_SIG_FREQ (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction attribute) MiXCRImport (class in immuneML.IO.dataset_import.MiXCRImport) ML_METHOD (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) ml_method (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) ml_method_name (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) MLMethodConfiguration (class in immuneML.IO.ml_method.MLMethodConfiguration) MLResult (class in immuneML.dsl.semantic_model.MLResult) model (immuneML.encodings.EncoderParams.EncoderParams attribute) MODEL_FILENAMES (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) model_path (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) ModelCreatorStrategy (class in immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy) ModelType (class in immuneML.encodings.word2vec.model_creator.ModelType) module immuneML immuneML.analysis immuneML.analysis.criteria_matches immuneML.analysis.criteria_matches.BooleanType immuneML.analysis.criteria_matches.CriteriaMatcher immuneML.analysis.criteria_matches.CriteriaTypeInstantiator 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.api immuneML.api.aggregated_runs immuneML.api.galaxy immuneML.api.galaxy.build_apply_gen_model_specs immuneML.api.galaxy.build_dummy_data_simulation_yaml immuneML.api.galaxy.build_ligo_yaml immuneML.app immuneML.caching immuneML.caching.CacheHandler immuneML.caching.CacheObjectType immuneML.caching.CacheType immuneML.data_model immuneML.data_model.AIRRSequenceSet immuneML.data_model.bnp_util immuneML.data_model.datasets immuneML.data_model.datasets.Dataset immuneML.data_model.datasets.ElementDataset immuneML.data_model.datasets.RepertoireDataset immuneML.data_model.EncodedData immuneML.data_model.SequenceParams immuneML.data_model.SequenceSet immuneML.dev_util immuneML.dev_util.util immuneML.dsl immuneML.dsl.DefaultParamsLoader immuneML.dsl.definition_parsers immuneML.dsl.definition_parsers.DefinitionParserOutput immuneML.dsl.definition_parsers.EncodingParser immuneML.dsl.definition_parsers.ExampleWeightingParser 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.import_parsers immuneML.dsl.import_parsers.ImportParser immuneML.dsl.instruction_parsers immuneML.dsl.instruction_parsers.DatasetExportParser immuneML.dsl.instruction_parsers.LabelHelper immuneML.dsl.instruction_parsers.SubsamplingParser immuneML.dsl.ObjectParser 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.dsl.Util immuneML.encodings immuneML.encodings.abundance_encoding immuneML.encodings.abundance_encoding.AbundanceEncoderHelper immuneML.encodings.abundance_encoding.CompAIRRBatchIterator immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder immuneML.encodings.atchley_kmer_encoding immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType immuneML.encodings.atchley_kmer_encoding.Util immuneML.encodings.DatasetEncoder immuneML.encodings.deeprc immuneML.encodings.deeprc.DeepRCEncoder immuneML.encodings.distance_encoding immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder immuneML.encodings.distance_encoding.DistanceEncoder immuneML.encodings.distance_encoding.DistanceMetricType immuneML.encodings.distance_encoding.TCRdistEncoder immuneML.encodings.EncoderParams immuneML.encodings.evenness_profile immuneML.encodings.evenness_profile.EvennessProfileEncoder immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder immuneML.encodings.kmer_frequency immuneML.encodings.kmer_frequency.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.kmer_frequency.sequence_encoding.VGeneContKmerEncoder immuneML.encodings.motif_encoding immuneML.encodings.motif_encoding.PositionalMotifParams immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder immuneML.encodings.onehot immuneML.encodings.onehot.OneHotEncoder immuneML.encodings.onehot.OneHotReceptorEncoder immuneML.encodings.onehot.OneHotRepertoireEncoder immuneML.encodings.onehot.OneHotSequenceEncoder immuneML.encodings.preprocessing immuneML.encodings.protein_embedding immuneML.encodings.reference_encoding immuneML.encodings.reference_encoding.MatchedReceptorsEncoder immuneML.encodings.reference_encoding.MatchedReferenceUtil immuneML.encodings.reference_encoding.MatchedRegexEncoder immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder immuneML.encodings.reference_encoding.MatchedSequencesEncoder immuneML.encodings.reference_encoding.SequenceMatchingSummaryType immuneML.encodings.word2vec immuneML.encodings.word2vec.model_creator immuneML.encodings.word2vec.model_creator.KmerPairModelCreator immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy immuneML.encodings.word2vec.model_creator.ModelType immuneML.encodings.word2vec.model_creator.SequenceModelCreator immuneML.environment immuneML.environment.Constants immuneML.environment.EnvironmentSettings immuneML.environment.Label immuneML.environment.LabelConfiguration immuneML.environment.LabelType immuneML.environment.SequenceType immuneML.example_weighting immuneML.example_weighting.ExampleWeightingParams immuneML.example_weighting.ExampleWeightingStrategy immuneML.example_weighting.predefined_weighting immuneML.example_weighting.predefined_weighting.PredefinedWeighting immuneML.hyperparameter_optimization immuneML.hyperparameter_optimization.config immuneML.hyperparameter_optimization.config.ClusterValidationType 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.states immuneML.hyperparameter_optimization.states.HPAssessmentState immuneML.hyperparameter_optimization.states.HPLabelState immuneML.hyperparameter_optimization.strategy immuneML.IO immuneML.IO.dataset_export immuneML.IO.dataset_export.AIRRExporter immuneML.IO.dataset_export.DataExporter immuneML.IO.dataset_import immuneML.IO.dataset_import.AIRRImport immuneML.IO.dataset_import.DataImport immuneML.IO.dataset_import.DatasetImportParams immuneML.IO.dataset_import.GenericImport immuneML.IO.dataset_import.IGoRImport immuneML.IO.dataset_import.ImmunoSEQRearrangementImport immuneML.IO.dataset_import.ImmunoSEQSampleImport immuneML.IO.dataset_import.IReceptorImport immuneML.IO.dataset_import.MiXCRImport immuneML.IO.dataset_import.OLGAImport immuneML.IO.dataset_import.RandomReceptorDatasetImport immuneML.IO.dataset_import.RandomRepertoireDatasetImport immuneML.IO.dataset_import.RandomSequenceDatasetImport immuneML.IO.dataset_import.TenxGenomicsImport immuneML.IO.dataset_import.VDJdbImport immuneML.IO.ml_method immuneML.IO.ml_method.MLMethodConfiguration immuneML.IO.ml_method.UtilIO immuneML.ml_methods immuneML.ml_methods.classifiers immuneML.ml_methods.clustering immuneML.ml_methods.clustering.ClusteringMethod immuneML.ml_methods.dim_reduction immuneML.ml_methods.dim_reduction.DimRedMethod immuneML.ml_methods.generative_models immuneML.ml_methods.generative_models.BackgroundSequences immuneML.ml_methods.generative_models.ExperimentalImport immuneML.ml_methods.generative_models.GenerativeModel immuneML.ml_methods.generative_models.InternalOlgaModel immuneML.ml_methods.generative_models.KLEvaluator immuneML.ml_methods.generative_models.MultinomialKmerModel immuneML.ml_methods.generative_models.OLGA immuneML.ml_methods.generative_models.PWM immuneML.ml_methods.generative_models.SequenceTransitionDistribution immuneML.ml_methods.generative_models.SimpleLSTM immuneML.ml_methods.generative_models.SoNNia immuneML.ml_methods.helper_methods immuneML.ml_methods.pytorch_implementations immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator immuneML.ml_methods.util immuneML.ml_methods.util.pytorch_util immuneML.ml_metrics immuneML.ml_metrics.ClassificationMetric immuneML.ml_metrics.ClusteringMetric 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.MetadataFilter immuneML.preprocessing.filters.SequenceLengthFilter immuneML.preprocessing.Preprocessor immuneML.preprocessing.ReferenceSequenceAnnotator immuneML.preprocessing.SubjectRepertoireCollector immuneML.presentation immuneML.presentation.html immuneML.presentation.html.FeasibilitySummaryHTMLBuilder immuneML.presentation.html.Util immuneML.presentation.InstructionPresentation immuneML.presentation.PresentationFormat immuneML.presentation.TemplateParser immuneML.reports immuneML.reports.clustering_method_reports immuneML.reports.clustering_method_reports.ClusteringMethodReport immuneML.reports.clustering_reports immuneML.reports.clustering_reports.ClusteringReport immuneML.reports.clustering_reports.ExternalLabelClusterSummary immuneML.reports.clustering_reports.ExternalLabelMetricHeatmap immuneML.reports.data_reports immuneML.reports.data_reports.DataReport immuneML.reports.data_reports.GLIPH2Exporter immuneML.reports.data_reports.LabelOverlap 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.gen_model_reports immuneML.reports.gen_model_reports.GenModelReport immuneML.reports.gen_model_reports.PWMSummary immuneML.reports.ml_reports immuneML.reports.ml_reports.CoefficientPlottingSetting immuneML.reports.ml_reports.CoefficientPlottingSettingList immuneML.reports.multi_dataset_reports immuneML.reports.PlotlyUtil immuneML.reports.Report immuneML.reports.ReportOutput immuneML.reports.ReportResult immuneML.reports.train_gen_model_reports immuneML.reports.train_gen_model_reports.KLKmerComparison immuneML.reports.train_gen_model_reports.TrainGenModelReport immuneML.reports.train_ml_model_reports immuneML.simulation immuneML.simulation.dataset_generation immuneML.simulation.dataset_generation.RandomDatasetGenerator immuneML.simulation.implants immuneML.simulation.implants.ImplantAnnotation immuneML.simulation.implants.LigoPWM immuneML.simulation.implants.Motif immuneML.simulation.implants.MotifInstance immuneML.simulation.implants.SeedMotif immuneML.simulation.implants.Signal immuneML.simulation.LigoSimState immuneML.simulation.SimConfig immuneML.simulation.SimConfigItem immuneML.simulation.simulation_strategy immuneML.simulation.simulation_strategy.ImplantingStrategy immuneML.simulation.simulation_strategy.RejectionSamplingStrategy immuneML.simulation.simulation_strategy.SimulationStrategy immuneML.simulation.util immuneML.simulation.util.bnp_util immuneML.simulation.util.igor_helper immuneML.simulation.util.util immuneML.util immuneML.util.AdaptiveImportHelper immuneML.util.CompAIRRHelper immuneML.util.CompAIRRParams immuneML.util.DistanceMetrics immuneML.util.DocEnumHelper immuneML.util.EncoderHelper immuneML.util.ExporterHelper immuneML.util.FilenameHandler immuneML.util.ImportHelper immuneML.util.KmerHelper immuneML.util.Logger immuneML.util.NameBuilder immuneML.util.NumpyHelper immuneML.util.ParameterValidator immuneML.util.PathBuilder immuneML.util.PositionHelper immuneML.util.ReadsType immuneML.util.ReflectionHandler immuneML.util.RepertoireBuilder immuneML.util.StringHelper immuneML.util.TCRdistHelper immuneML.workflows immuneML.workflows.instructions immuneML.workflows.instructions.apply_gen_model immuneML.workflows.instructions.clustering immuneML.workflows.instructions.clustering.clustering_run_model immuneML.workflows.instructions.clustering.ClusteringReportHandler immuneML.workflows.instructions.clustering.ClusteringState immuneML.workflows.instructions.dataset_generation immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction immuneML.workflows.instructions.dataset_generation.DatasetExportState immuneML.workflows.instructions.exploratory_analysis immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit immuneML.workflows.instructions.Instruction immuneML.workflows.instructions.ligo_sim_feasibility immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction immuneML.workflows.instructions.ligo_simulation immuneML.workflows.instructions.ligo_simulation.runtime_reports immuneML.workflows.instructions.ml_model_application immuneML.workflows.instructions.subsampling immuneML.workflows.instructions.subsampling.SubsamplingInstruction immuneML.workflows.instructions.subsampling.SubsamplingState immuneML.workflows.instructions.train_gen_model immuneML.workflows.steps immuneML.workflows.steps.data_splitter 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.DataWeighter immuneML.workflows.steps.DataWeighterParams immuneML.workflows.steps.Step immuneML.workflows.steps.StepParams

MORISITA_HORN (immuneML.encodings.distance_encoding.DistanceMetricType.DistanceMetricType attribute) morisita_horn() (in module immuneML.util.DistanceMetrics) Motif (class in immuneML.simulation.implants.Motif) MOTIF (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) motif_id (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) motif_instance (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) MotifInstance (class in immuneML.simulation.implants.MotifInstance) MotifInstanceGroup (class in immuneML.simulation.implants.MotifInstance) MotifParser (class in immuneML.dsl.definition_parsers.MotifParser) motifs (immuneML.simulation.implants.Signal.Signal attribute) mu (immuneML.ml_methods.generative_models.MultinomialKmerModel.Poisson attribute) MultinomialKmerModel (class in immuneML.ml_methods.generative_models.MultinomialKmerModel)

N

N_LARGEST (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) name (immuneML.data_model.datasets.Dataset.Dataset attribute) (immuneML.reports.ReportResult.ReportResult attribute) (immuneML.simulation.LigoSimState.LigoSimState attribute) (immuneML.simulation.SimConfigItem.SimConfigItem attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) NameBuilder (class in immuneML.util.NameBuilder)

needs_seqs_with_signal() (in module immuneML.simulation.util.util) no_gaps (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams attribute) NONE (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) NONZERO (immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting attribute) NormalizationType (class in immuneML.analysis.data_manipulation.NormalizationType) 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) number_of_examples (immuneML.simulation.SimConfigItem.SimConfigItem attribute) number_of_processes (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) NumpyHelper (class in immuneML.util.NumpyHelper)

O

ObjectParser (class in immuneML.dsl.ObjectParser) OLGA (class in immuneML.ml_methods.generative_models.OLGA) olga_gen_model (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) OLGAImport (class in immuneML.IO.dataset_import.OLGAImport) OneHotEncoder (class in immuneML.encodings.onehot.OneHotEncoder) OneHotReceptorEncoder (class in immuneML.encodings.onehot.OneHotReceptorEncoder) OneHotRepertoireEncoder (class in immuneML.encodings.onehot.OneHotRepertoireEncoder) OneHotSequenceEncoder (class in immuneML.encodings.onehot.OneHotSequenceEncoder) OperationType (class in immuneML.analysis.criteria_matches.OperationType) optimal_assessment_item (immuneML.hyperparameter_optimization.states.HPLabelState.HPLabelState property) optimal_hp_setting (immuneML.hyperparameter_optimization.states.HPLabelState.HPLabelState property) 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) original_plot() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) OTHER (immuneML.caching.CacheObjectType.CacheObjectType attribute) OUTPUT (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) OUTPUT_COLUMNS (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel attribute) (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) output_figures (immuneML.reports.ReportResult.ReportResult attribute) OUTPUT_FILENAME (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder attribute) output_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) output_pairs (immuneML.util.CompAIRRParams.CompAIRRParams attribute) output_tables (immuneML.reports.ReportResult.ReportResult attribute) output_text (immuneML.reports.ReportResult.ReportResult attribute)

P

p_gen_bin_count (immuneML.simulation.SimConfig.SimConfig attribute) p_gen_bins (immuneML.simulation.LigoSimState.LigoSimState attribute) p_gen_histogram (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) pad_ragged_array() (in module immuneML.simulation.util.bnp_util) pad_sequence_in_the_middle() (immuneML.util.StringHelper.StringHelper static method) paired (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.simulation.SimConfig.SimConfig attribute) pairs_filename (immuneML.util.CompAIRRParams.CompAIRRParams attribute) PairwiseRepertoireComparison (class in immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison) parameter (immuneML.hyperparameter_optimization.config.LeaveOneOutConfig.LeaveOneOutConfig attribute) ParameterValidator (class in immuneML.util.ParameterValidator) parse() (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser static method) (immuneML.dsl.definition_parsers.ExampleWeightingParser.ExampleWeightingParser static method) (immuneML.dsl.definition_parsers.MotifParser.MotifParser static method) (immuneML.dsl.definition_parsers.PreprocessingParser.PreprocessingParser static method) (immuneML.dsl.definition_parsers.ReportParser.ReportParser static method) (immuneML.dsl.definition_parsers.SignalParser.SignalParser static method) (immuneML.dsl.definition_parsers.SimulationParser.SimulationParser static method) (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) (immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser method) (immuneML.dsl.instruction_parsers.SubsamplingParser.SubsamplingParser method) (immuneML.dsl.Parser.Parser method) (immuneML.presentation.TemplateParser.TemplateParser static method) parse_adaptive_germline_to_imgt() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) parse_allele() (in module immuneML.util.AdaptiveImportHelper) parse_command_line_arguments() (in module immuneML.api.galaxy.build_apply_gen_model_specs) (in module immuneML.api.galaxy.build_ligo_yaml) parse_commandline_arguments() (in module immuneML.api.galaxy.build_dummy_data_simulation_yaml) parse_criteria() (immuneML.analysis.criteria_matches.CriteriaMatcher.CriteriaMatcher static method) parse_dataset() (immuneML.dsl.import_parsers.ImportParser.ImportParser static method) parse_encoder() (immuneML.dsl.definition_parsers.EncodingParser.EncodingParser static method) parse_exporters() (in module immuneML.dsl.Util) parse_gene_column() (in module immuneML.util.AdaptiveImportHelper) parse_germline() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) parse_object() (immuneML.dsl.ObjectParser.ObjectParser static method) parse_weighting_strategy() (immuneML.dsl.definition_parsers.ExampleWeightingParser.ExampleWeightingParser static method) Parser (class in immuneML.dsl.Parser) path (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) (immuneML.presentation.InstructionPresentation.InstructionPresentation attribute) (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringSetting attribute) PathBuilder (class in immuneML.util.PathBuilder) paths (immuneML.simulation.LigoSimState.LigoSimState attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) PERCENTAGE (immuneML.encodings.reference_encoding.SequenceMatchingSummaryType.SequenceMatchingSummaryType attribute) PLOTLY_BLACK (immuneML.environment.Constants.Constants attribute) PlotlyUtil (class in immuneML.reports.PlotlyUtil) Poisson (class in immuneML.ml_methods.generative_models.MultinomialKmerModel) pool_size (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.encodings.motif_encoding.PositionalMotifParams.PositionalMotifParams attribute) (immuneML.example_weighting.ExampleWeightingParams.ExampleWeightingParams attribute) position (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute) position_weights (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) PositionalMotifParams (class in immuneML.encodings.motif_encoding.PositionalMotifParams) PositionHelper (class in immuneML.util.PositionHelper) positive_class (immuneML.environment.Label.Label property)

PRECISION (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) PredefinedWeighting (class in immuneML.example_weighting.predefined_weighting.PredefinedWeighting) predict() (immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod method) predictions (immuneML.workflows.instructions.clustering.clustering_run_model.ClusteringItem attribute) predictions_paths (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) prepare_caching_params() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) prepare_data_for_airr_seq_set() (in module immuneML.simulation.util.util) prepare_data_for_repertoire_obj() (in module immuneML.simulation.util.util) prepare_paralellization_arguments() (immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison.PairwiseRepertoireComparison method) prepare_path() (immuneML.workflows.steps.data_splitter.Util.Util static method) prepare_reference() (immuneML.encodings.reference_encoding.MatchedReferenceUtil.MatchedReferenceUtil static method) prepare_tcr_dist_dataframe() (immuneML.util.TCRdistHelper.TCRdistHelper static method) prepare_training_ids() (immuneML.util.EncoderHelper.EncoderHelper static method) prepare_values_for_bnp() (in module immuneML.data_model.bnp_util) preprocess_dataframe() (immuneML.util.AdaptiveImportHelper.AdaptiveImportHelper static method) preprocess_dataset() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) preprocess_file() (immuneML.IO.dataset_import.DataImport.DataImport method) (immuneML.IO.dataset_import.IGoRImport.IGoRImport method) (immuneML.IO.dataset_import.ImmunoSEQRearrangementImport.ImmunoSEQRearrangementImport method) (immuneML.IO.dataset_import.ImmunoSEQSampleImport.ImmunoSEQSampleImport method) (immuneML.IO.dataset_import.MiXCRImport.MiXCRImport method) (immuneML.IO.dataset_import.VDJdbImport.VDJdbImport method) PREPROCESSED (immuneML.data_model.datasets.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) PresentationFormat (class in immuneML.presentation.PresentationFormat) print_log() (in module immuneML.util.Logger) process_and_store_data_file() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) process_and_store_dataset_file() (immuneML.IO.dataset_export.AIRRExporter.AIRRExporter static method) process_compairr_output_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) process_dataset() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) (immuneML.preprocessing.filters.ChainRepertoireFilter.ChainRepertoireFilter method) (immuneML.preprocessing.filters.ClonesPerRepertoireFilter.ClonesPerRepertoireFilter method) (immuneML.preprocessing.filters.CountPerSequenceFilter.CountPerSequenceFilter method) (immuneML.preprocessing.filters.DuplicateSequenceFilter.DuplicateSequenceFilter method) (immuneML.preprocessing.filters.MetadataFilter.MetadataFilter method) (immuneML.preprocessing.filters.SequenceLengthFilter.SequenceLengthFilter method) (immuneML.preprocessing.Preprocessor.Preprocessor method) (immuneML.preprocessing.ReferenceSequenceAnnotator.ReferenceSequenceAnnotator method) (immuneML.preprocessing.SubjectRepertoireCollector.SubjectRepertoireCollector method) process_repertoire() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) process_sequences() (immuneML.simulation.simulation_strategy.ImplantingStrategy.ImplantingStrategy method) (immuneML.simulation.simulation_strategy.RejectionSamplingStrategy.RejectionSamplingStrategy method) (immuneML.simulation.simulation_strategy.SimulationStrategy.SimulationStrategy method) PRODUCTION (immuneML.caching.CacheType.CacheType attribute) productive (immuneML.data_model.SequenceSet.ReceptorSequence attribute) PWM (class in immuneML.ml_methods.generative_models.PWM) pwm_matrix (immuneML.simulation.implants.LigoPWM.LigoPWM attribute) PWMSummary (class in immuneML.reports.gen_model_reports.PWMSummary) PyTorchLogisticRegression (class in immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression) PyTorchReceptorCNN (class in immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN)

R

RANDOM (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) RANDOM_N (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) RandomDatasetGenerator (class in immuneML.simulation.dataset_generation.RandomDatasetGenerator) RandomReceptorDatasetImport (class in immuneML.IO.dataset_import.RandomReceptorDatasetImport) RandomRepertoireDatasetImport (class in immuneML.IO.dataset_import.RandomRepertoireDatasetImport) RandomSequenceDatasetImport (class in immuneML.IO.dataset_import.RandomSequenceDatasetImport) raw() (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.EncodedLookup method) read_compairr_output_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) read_yaml() (in module immuneML.data_model.bnp_util) ReadsType (class in immuneML.util.ReadsType) RECALL (immuneML.ml_metrics.ClassificationMetric.ClassificationMetric attribute) Receptor (class in immuneML.data_model.SequenceSet) receptor_chains (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) receptor_id (immuneML.data_model.SequenceSet.Receptor attribute) ReceptorDataset (class in immuneML.data_model.datasets.ElementDataset) ReceptorDatasetOverview (class in immuneML.reports.data_reports.ReceptorDatasetOverview) receptors() (immuneML.data_model.SequenceSet.Repertoire method) receptors_in_repertoire_count (immuneML.simulation.SimConfigItem.SimConfigItem attribute) ReceptorSequence (class in immuneML.data_model.SequenceSet) ReductionMethod (class in immuneML.analysis.data_manipulation.ReductionMethod) ReferenceSequenceAnnotator (class in immuneML.preprocessing.ReferenceSequenceAnnotator) ReflectionHandler (class in immuneML.util.ReflectionHandler) region_type (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.ml_methods.generative_models.OLGA.OLGA attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) RegionType (class in immuneML.data_model.SequenceParams) REGRESSION (immuneML.environment.LabelType.LabelType attribute) RejectionSamplingStrategy (class in immuneML.simulation.simulation_strategy.RejectionSamplingStrategy) RELATIVE_ABUNDANCE (immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType.RelativeAbundanceType attribute) RELATIVE_FREQUENCY (immuneML.analysis.data_manipulation.NormalizationType.NormalizationType attribute) RelativeAbundanceType (class in immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType) RELEVANT_SEQUENCE_ABUNDANCE (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder attribute) RelevantSequenceExporter (class in immuneML.reports.encoding_reports.RelevantSequenceExporter) remove_illegal_chains() (immuneML.util.ImportHelper.ImportHelper static method) remove_old_and_build() (immuneML.util.PathBuilder.PathBuilder static method) remove_seqs_with_signals (immuneML.simulation.SimConfig.SimConfig attribute) renyi_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) Repertoire (class in immuneML.data_model.SequenceSet) repertoire_index_mapping (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch attribute) RepertoireBuilder (class in immuneML.util.RepertoireBuilder) RepertoireDataset (class in immuneML.data_model.datasets.RepertoireDataset) REPERTOIRES_FOLDER (immuneML.IO.dataset_import.IReceptorImport.IReceptorImport attribute) replace_nans_with_empty_str() (in module immuneML.util.AdaptiveImportHelper) Report (class in immuneML.reports.Report)

REPORT (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) report_p_gen_histogram() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_results (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringItemResult attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) report_seq_len_dist() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_cond_probs() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_cooccurrences() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_frequencies() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) report_signal_joint_probs() (in module immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports) ReportConfig (class in immuneML.hyperparameter_optimization.config.ReportConfig) ReportOutput (class in immuneML.reports.ReportOutput) ReportParser (class in immuneML.dsl.definition_parsers.ReportParser) ReportResult (class in immuneML.reports.ReportResult) reports (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit.ExploratoryAnalysisUnit attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) REQUIRED_KEYS (immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser attribute) rescale_weights_for_IGM() (immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN.PyTorchReceptorCNN method) reset_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) reshape() (immuneML.analysis.data_manipulation.DataReshaper.DataReshaper static method) result_based_validation (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResults attribute) result_path (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.example_weighting.ExampleWeightingParams.ExampleWeightingParams attribute) (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) (immuneML.simulation.LigoSimState.LigoSimState attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) (immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState attribute) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) resulting_dataset (immuneML.simulation.LigoSimState.LigoSimState attribute) root_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) run() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) (immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction.DatasetExportInstruction method) (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) (immuneML.workflows.instructions.Instruction.Instruction method) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryInstruction method) (immuneML.workflows.instructions.subsampling.SubsamplingInstruction.SubsamplingInstruction method) (immuneML.workflows.steps.DataEncoder.DataEncoder static method) (immuneML.workflows.steps.DataWeighter.DataWeighter static method) (immuneML.workflows.steps.Step.Step static method) run_clustering_reports() (immuneML.workflows.instructions.clustering.ClusteringReportHandler.ClusteringReportHandler method) run_id (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun attribute) run_instructions() (immuneML.dsl.semantic_model.SemanticModel.SemanticModel method) run_item_reports() (immuneML.workflows.instructions.clustering.ClusteringReportHandler.ClusteringReportHandler method) run_report() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) run_type (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringResultPerRun attribute) run_unit() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method)

S

sample() (immuneML.ml_methods.generative_models.MultinomialKmerModel.EmpiricalLengthDistribution method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.KmerDistribution method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.KmerModel method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.MultinomialKmerModel method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.Poisson method) (immuneML.ml_methods.generative_models.MultinomialKmerModel.SmoothedLengthDistribution method) (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution method) save() (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution method) save_model() (immuneML.ml_methods.generative_models.GenerativeModel.GenerativeModel method) (immuneML.ml_methods.generative_models.OLGA.OLGA method) (immuneML.ml_methods.generative_models.PWM.PWM method) (immuneML.ml_methods.generative_models.SimpleLSTM.SimpleLSTM method) (immuneML.ml_methods.generative_models.SoNNia.SoNNia method) seed (immuneML.simulation.implants.SeedMotif.SeedMotif attribute) (immuneML.simulation.SimConfigItem.SimConfigItem attribute) SeedMotif (class in immuneML.simulation.implants.SeedMotif) sem() (immuneML.reports.encoding_reports.FeatureReport.FeatureReport method) SemanticModel (class in immuneML.dsl.semantic_model.SemanticModel) SEP (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) separator (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) seq_len_dist (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) sequence (immuneML.data_model.SequenceSet.ReceptorSequence attribute) SEQUENCE (immuneML.encodings.word2vec.model_creator.ModelType.ModelType attribute) sequence_aa (immuneML.data_model.SequenceSet.ReceptorSequence attribute) SEQUENCE_COLUMN (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder attribute) sequence_count (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) sequence_file_size (immuneML.IO.dataset_import.DatasetImportParams.DatasetImportParams attribute) sequence_gen_model (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) sequence_id (immuneML.data_model.SequenceSet.ReceptorSequence attribute) sequence_len_limits (immuneML.simulation.SimConfigItem.SimConfigItem attribute) sequence_position_weights (immuneML.simulation.implants.Signal.Signal attribute) sequence_type (immuneML.encodings.EncoderParams.EncoderParams attribute) (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) (immuneML.simulation.SimConfig.SimConfig attribute) (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) SequenceAbundanceEncoder (class in immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder) SequenceDataset (class in immuneML.data_model.datasets.ElementDataset) SequenceEncodingStrategy (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy) SequenceEncodingType (class in immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType) SequenceLengthDistribution (class in immuneML.reports.data_reports.SequenceLengthDistribution) SequenceLengthFilter (class in immuneML.preprocessing.filters.SequenceLengthFilter) SequenceMatcher (class in immuneML.analysis.SequenceMatcher) SequenceMatchingSummaryType (class in immuneML.encodings.reference_encoding.SequenceMatchingSummaryType) SequenceModelCreator (class in immuneML.encodings.word2vec.model_creator.SequenceModelCreator) sequences() (immuneML.data_model.SequenceSet.Repertoire method) SequenceTransitionDistribution (class in immuneML.ml_methods.generative_models.SequenceTransitionDistribution) SequenceType (class in immuneML.environment.SequenceType) set_cache_path() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) set_context() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder method) (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.encodings.deeprc.DeepRCEncoder.DeepRCEncoder method) (immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder.CompAIRRDistanceEncoder method) (immuneML.encodings.distance_encoding.DistanceEncoder.DistanceEncoder method) (immuneML.encodings.distance_encoding.TCRdistEncoder.TCRdistEncoder method) (immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder.SimilarToPositiveSequenceEncoder method) (immuneML.example_weighting.ExampleWeightingStrategy.ExampleWeightingStrategy method) (immuneML.reports.Report.Report method) set_default_weights() (immuneML.simulation.implants.SeedMotif.SeedMotif method) set_iteration_repertoire_ids() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) set_locus_column() (in module immuneML.util.AdaptiveImportHelper) set_repertoire_ids() (immuneML.encodings.abundance_encoding.CompAIRRBatchIterator.CompAIRRBatchIterator method) set_sequence_type() (immuneML.environment.EnvironmentSettings.EnvironmentSettings static method) shannon_entropy() (immuneML.analysis.entropy_calculations.EntropyCalculator.EntropyCalculator static method) Signal (class in immuneML.simulation.implants.Signal) SIGNAL (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) signal1 (immuneML.simulation.implants.Signal.SignalPair attribute) signal2 (immuneML.simulation.implants.Signal.SignalPair attribute) signal_cond_probs (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) signal_cooccurrences (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) SIGNAL_DELIMITER (immuneML.environment.Constants.Constants attribute) signal_frequencies (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) signal_id (immuneML.simulation.implants.ImplantAnnotation.ImplantAnnotation attribute)

signal_joint_probs (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) signal_proportions (immuneML.simulation.SimConfigItem.SimConfigItem attribute) SignalPair (class in immuneML.simulation.implants.Signal) SignalParser (class in immuneML.dsl.definition_parsers.SignalParser) signals (immuneML.simulation.LigoSimState.LigoSimState attribute) (immuneML.simulation.SimConfigItem.SimConfigItem property) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) sim_items (immuneML.simulation.SimConfig.SimConfig attribute) SimConfig (class in immuneML.simulation.SimConfig) SimConfigItem (class in immuneML.simulation.SimConfigItem) SimilarToPositiveSequenceEncoder (class in immuneML.encodings.motif_encoding.SimilarToPositiveSequenceEncoder) SIMPLE_TYPES (immuneML.util.NumpyHelper.NumpyHelper attribute) SimpleDatasetOverview (class in immuneML.reports.data_reports.SimpleDatasetOverview) SimpleLSTM (class in immuneML.ml_methods.generative_models.SimpleLSTM) SimpleLSTMGenerator (class in immuneML.ml_methods.pytorch_implementations.SimpleLSTMGenerator) SimpleVAEGenerator (class in immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator) simulated_kl() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) simulated_kl_weights() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) simulated_plot() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) SIMULATION (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) simulation (immuneML.simulation.LigoSimState.LigoSimState attribute) (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySummaryState attribute) simulation_strategy (immuneML.simulation.SimConfig.SimConfig attribute) SimulationParser (class in immuneML.dsl.definition_parsers.SimulationParser) SimulationStrategy (class in immuneML.simulation.simulation_strategy.SimulationStrategy) SmoothedLengthDistribution (class in immuneML.ml_methods.generative_models.MultinomialKmerModel) software_used (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration attribute) SoNNia (class in immuneML.ml_methods.generative_models.SoNNia) source_docs_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) species (immuneML.simulation.SimConfig.SimConfig attribute) specs_docs_path (immuneML.environment.EnvironmentSettings.EnvironmentSettings attribute) split_config (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) split_count (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) split_dataset() (immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter.LeaveOneOutSplitter static method) (immuneML.workflows.steps.data_splitter.ManualSplitter.ManualSplitter static method) 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) standardize_bool_values() (immuneML.util.ImportHelper.ImportHelper static method) standardize_column_names() (immuneML.util.ImportHelper.ImportHelper static method) standardize_none_values() (immuneML.util.ImportHelper.ImportHelper static method) std() (immuneML.reports.encoding_reports.FeatureReport.FeatureReport method) Step (class in immuneML.workflows.steps.Step) STEP_ENCODED (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) STEP_VECTORIZED (immuneML.encodings.evenness_profile.EvennessProfileEncoder.EvennessProfileEncoder attribute) StepParams (class in immuneML.workflows.steps.StepParams) stop_codon (immuneML.data_model.SequenceSet.ReceptorSequence attribute) STOP_CODON (immuneML.environment.Constants.Constants attribute) store() (immuneML.encodings.DatasetEncoder.DatasetEncoder method) (immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration method) (immuneML.pairwise_repertoire_comparison.ComparisonDataBatch.ComparisonDataBatch method) store_encoder() (immuneML.encodings.DatasetEncoder.DatasetEncoder static method) store_tmp_batch() (immuneML.pairwise_repertoire_comparison.ComparisonData.ComparisonData method) store_weights() (in module immuneML.ml_methods.util.pytorch_util) strategy_supports_signals() (in module immuneML.dsl.definition_parsers.SimulationParser) STRATIFIED_K_FOLD (immuneML.hyperparameter_optimization.config.SplitType.SplitType attribute) StringHelper (class in immuneML.util.StringHelper) SubjectRepertoireCollector (class in immuneML.preprocessing.SubjectRepertoireCollector) SUBSAMPLED (immuneML.data_model.datasets.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) subsampled_repertoire_size (immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState attribute) 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) 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

target_p_gen_histogram (immuneML.simulation.LigoSimState.LigoSimState attribute) TCRB_RELATIVE_ABUNDANCE (immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType.RelativeAbundanceType attribute) TCRdistEncoder (class in immuneML.encodings.distance_encoding.TCRdistEncoder) TCRdistHelper (class in immuneML.util.TCRdistHelper) TemplateParser (class in immuneML.presentation.TemplateParser) TenxGenomicsImport (class in immuneML.IO.dataset_import.TenxGenomicsImport) TEST (immuneML.caching.CacheType.CacheType attribute) (immuneML.data_model.datasets.Dataset.Dataset attribute) test_metadata_path (immuneML.hyperparameter_optimization.config.ManualSplitConfig.ManualSplitConfig attribute) threads (immuneML.util.CompAIRRParams.CompAIRRParams attribute) threshold (immuneML.simulation.implants.LigoPWM.LigoPWM 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) to_string() (immuneML.data_model.SequenceParams.Chain method) (immuneML.data_model.SequenceParams.RegionType method)

TOP_N (immuneML.analysis.criteria_matches.OperationType.OperationType attribute) TOTAL_SEQUENCE_ABUNDANCE (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder attribute) (immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder.SequenceAbundanceEncoder attribute) TRA_TRB (immuneML.data_model.SequenceParams.ChainPair attribute) TRAIN (immuneML.data_model.datasets.Dataset.Dataset 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) TrainGenModelReport (class in immuneML.reports.train_gen_model_reports.TrainGenModelReport) training_percentage (immuneML.workflows.steps.data_splitter.DataSplitterParams.DataSplitterParams attribute) transform() (immuneML.ml_methods.clustering.ClusteringMethod.ClusteringMethod method) (immuneML.ml_methods.dim_reduction.DimRedMethod.DimRedMethod method) transition_matrix (immuneML.ml_methods.generative_models.SequenceTransitionDistribution.SequenceTransitionDistribution attribute) translate_sequence() (immuneML.IO.dataset_import.IGoRImport.IGoRImport static method) TRG_TRD (immuneML.data_model.SequenceParams.ChainPair attribute) true_kl() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method) true_kl_weights() (immuneML.ml_methods.generative_models.KLEvaluator.KLEvaluator method)

U

UniformLinear (class in immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator) UNIQUE (immuneML.util.ReadsType.ReadsType attribute) UNKNOWN (immuneML.environment.Constants.Constants attribute) UNKNOWN_CHAIN (immuneML.reports.data_reports.SimpleDatasetOverview.SimpleDatasetOverview attribute) update_report_paths() (immuneML.presentation.html.Util.Util static method)

update_seqs_with_signal() (in module immuneML.simulation.util.util) update_seqs_without_signal() (in module immuneML.simulation.util.util) Util (class in immuneML.encodings.atchley_kmer_encoding.Util) (class in immuneML.presentation.html.Util) (class in immuneML.workflows.steps.data_splitter.Util) UtilIO (class in immuneML.IO.ml_method.UtilIO)

V

v_call (immuneML.data_model.SequenceSet.ReceptorSequence attribute) (immuneML.simulation.implants.Signal.Signal attribute) (immuneML.simulation.implants.Signal.SignalPair property) v_gene (immuneML.data_model.SequenceSet.ReceptorSequence property) V_GENE_CONT_KMER (immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType attribute) v_gene_mapping (immuneML.ml_methods.generative_models.InternalOlgaModel.InternalOlgaModel attribute) vae_cdr3_loss() (in module immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator) valid_keys (immuneML.dsl.import_parsers.ImportParser.ImportParser attribute)

validation_datasets (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringState attribute) validation_type (immuneML.workflows.instructions.clustering.ClusteringState.ClusteringConfig attribute) values (immuneML.environment.Label.Label property) VDJdbImport (class in immuneML.IO.dataset_import.VDJdbImport) verify_compairr_output_path() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) VERSION (immuneML.environment.Constants.Constants attribute) VGeneContKmerEncoder (class in immuneML.encodings.kmer_frequency.sequence_encoding.VGeneContKmerEncoder) vj_in_frame (immuneML.data_model.SequenceSet.ReceptorSequence attribute)

W

warn_deprecated_parameter() (immuneML.util.ParameterValidator.ParameterValidator class method) warnings (immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction.FeasibilitySumReports attribute) weight_examples() (immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction.ExploratoryAnalysisInstruction method) WEIGHTING (immuneML.dsl.symbol_table.SymbolType.SymbolType attribute) weighting_params (immuneML.workflows.steps.DataWeighterParams.DataWeighterParams attribute) weighting_strategy (immuneML.workflows.steps.DataWeighterParams.DataWeighterParams attribute)

write_bnp_data() (in module immuneML.simulation.util.util) write_dataset_yaml() (in module immuneML.data_model.bnp_util) write_image_to_file() (immuneML.reports.PlotlyUtil.PlotlyUtil static method) write_repertoire_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) write_sequence_set_file() (immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder.CompAIRRSequenceAbundanceEncoder method) write_sequences_file() (immuneML.util.CompAIRRHelper.CompAIRRHelper static method) write_yaml() (in module immuneML.data_model.bnp_util)

X

XavierLinear (class in immuneML.ml_methods.pytorch_implementations.SimpleVAEGenerator)