immuneML package

Subpackages

• immuneML.IO package
  • Subpackages
    • immuneML.IO.dataset_export package
      • Submodules
      • immuneML.IO.dataset_export.AIRRExporter module
      • immuneML.IO.dataset_export.DataExporter module
      • immuneML.IO.dataset_export.ImmuneMLExporter module
      • Module contents
    • immuneML.IO.dataset_import package
      • Submodules
      • 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.IReceptorImport module
      • immuneML.IO.dataset_import.ImmuneMLImport module
      • immuneML.IO.dataset_import.ImmunoSEQRearrangementImport module
      • immuneML.IO.dataset_import.ImmunoSEQSampleImport module
      • immuneML.IO.dataset_import.MiXCRImport module
      • immuneML.IO.dataset_import.OLGAImport module
      • immuneML.IO.dataset_import.RandomReceptorDatasetImport module
      • immuneML.IO.dataset_import.RandomRepertoireDatasetImport module
      • immuneML.IO.dataset_import.RandomSequenceDatasetImport module
      • immuneML.IO.dataset_import.SingleLineReceptorImport module
      • immuneML.IO.dataset_import.TenxGenomicsImport module
      • immuneML.IO.dataset_import.VDJdbImport module
      • Module contents
    • immuneML.IO.ml_method package
      • Submodules
      • immuneML.IO.ml_method.MLExporter module
      • immuneML.IO.ml_method.MLImport module
      • immuneML.IO.ml_method.MLMethodConfiguration module
      • immuneML.IO.ml_method.UtilIO module
      • Module contents
  • Module contents
• immuneML.analysis package
  • Subpackages
    • immuneML.analysis.criteria_matches package
      • Submodules
      • immuneML.analysis.criteria_matches.BooleanType module
      • immuneML.analysis.criteria_matches.CriteriaMatcher module
      • immuneML.analysis.criteria_matches.CriteriaTypeInstantiator module
      • immuneML.analysis.criteria_matches.DataType module
      • immuneML.analysis.criteria_matches.OperationType module
      • Module contents
    • immuneML.analysis.data_manipulation package
      • Submodules
      • immuneML.analysis.data_manipulation.DataReshaper module
      • immuneML.analysis.data_manipulation.NormalizationType module
      • immuneML.analysis.data_manipulation.ReductionMethod module
      • Module contents
    • immuneML.analysis.entropy_calculations package
      • Submodules
      • immuneML.analysis.entropy_calculations.EntropyCalculator module
      • Module contents
    • immuneML.analysis.similarities package
      • Submodules
      • immuneML.analysis.similarities.SimilarityMeasureType module
      • Module contents
  • Submodules
  • immuneML.analysis.AxisType module
    • AxisType
      • AxisType.FEATURES
      • AxisType.REPERTOIRES
  • immuneML.analysis.SequenceMatcher module
    • SequenceMatcher
      • SequenceMatcher.CORES
      • SequenceMatcher.match()
      • SequenceMatcher.match_repertoire()
      • SequenceMatcher.match_sequence()
      • SequenceMatcher.matches_gene()
      • SequenceMatcher.matches_sequence()
  • Module contents
• immuneML.api package
  • Subpackages
    • immuneML.api.aggregated_runs package
      • Submodules
      • immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool module
      • Module contents
    • immuneML.api.galaxy package
      • Submodules
      • immuneML.api.galaxy.DataSimulationTool module
      • immuneML.api.galaxy.DatasetGenerationTool module
      • immuneML.api.galaxy.GalaxyMLApplicationTool module
      • immuneML.api.galaxy.GalaxySimulationTool module
      • immuneML.api.galaxy.GalaxyTool module
      • immuneML.api.galaxy.GalaxyTrainMLModel module
      • immuneML.api.galaxy.GalaxyYamlTool module
      • immuneML.api.galaxy.RepertoireClassificationTool module
      • immuneML.api.galaxy.Util module
      • immuneML.api.galaxy.build_dataset_yaml module
      • immuneML.api.galaxy.build_yaml_from_arguments module
      • Module contents
  • Submodules
  • immuneML.api.api_encoding module
    • encode_dataset_by_kmer_freq()
    • generate_random_metadata()
  • Module contents
• immuneML.app package
  • Submodules
  • immuneML.app.ImmuneMLApp module
    • ImmuneMLApp
      • ImmuneMLApp.clear_cache()
      • ImmuneMLApp.run()
      • ImmuneMLApp.set_cache()
    • main()
    • run_immuneML()
  • Module contents
• immuneML.caching package
  • Submodules
  • immuneML.caching.CacheHandler module
    • CacheHandler
      • CacheHandler.add()
      • CacheHandler.add_by_key()
      • CacheHandler.exists()
      • CacheHandler.generate_cache_key()
      • CacheHandler.get()
      • CacheHandler.get_by_key()
      • CacheHandler.get_file_path()
      • CacheHandler.memo()
      • CacheHandler.memo_by_params()
  • immuneML.caching.CacheObjectType module
    • CacheObjectType
      • CacheObjectType.ENCODING
      • CacheObjectType.ENCODING_STEP
      • CacheObjectType.OTHER
  • immuneML.caching.CacheType module
    • CacheType
      • CacheType.PRODUCTION
      • CacheType.TEST
  • Module contents
• immuneML.data_model package
  • Subpackages
    • immuneML.data_model.cell package
      • Submodules
      • immuneML.data_model.cell.Cell module
      • immuneML.data_model.cell.CellList module
      • Module contents
    • immuneML.data_model.dataset package
      • Submodules
      • immuneML.data_model.dataset.Dataset module
      • immuneML.data_model.dataset.ElementDataset module
      • immuneML.data_model.dataset.ReceptorDataset module
      • immuneML.data_model.dataset.RepertoireDataset module
      • immuneML.data_model.dataset.SequenceDataset module
      • Module contents
    • immuneML.data_model.encoded_data package
      • Submodules
      • immuneML.data_model.encoded_data.EncodedData module
      • Module contents
    • immuneML.data_model.receptor package
      • Subpackages
      • Submodules
      • immuneML.data_model.receptor.BCKReceptor module
      • immuneML.data_model.receptor.BCReceptor module
      • immuneML.data_model.receptor.ChainPair module
      • immuneML.data_model.receptor.ElementGenerator module
      • immuneML.data_model.receptor.Receptor module
      • immuneML.data_model.receptor.ReceptorBuilder module
      • immuneML.data_model.receptor.RegionType module
      • immuneML.data_model.receptor.TCABReceptor module
      • immuneML.data_model.receptor.TCGDReceptor module
      • Module contents
    • immuneML.data_model.repertoire package
      • Submodules
      • immuneML.data_model.repertoire.Repertoire module
      • Module contents
  • Submodules
  • immuneML.data_model.DatasetItem module
  • Module contents
• immuneML.dev_util package
  • Submodules
  • immuneML.dev_util.util module
    • load_encoded_data()
  • Module contents
• immuneML.dsl package
  • Subpackages
    • immuneML.dsl.definition_parsers package
      • Submodules
      • immuneML.dsl.definition_parsers.DefinitionParser module
      • immuneML.dsl.definition_parsers.DefinitionParserOutput module
      • immuneML.dsl.definition_parsers.EncodingParser module
      • immuneML.dsl.definition_parsers.MLParser module
      • immuneML.dsl.definition_parsers.MotifParser module
      • immuneML.dsl.definition_parsers.PreprocessingParser module
      • immuneML.dsl.definition_parsers.ReportParser module
      • immuneML.dsl.definition_parsers.SignalParser module
      • immuneML.dsl.definition_parsers.SimulationParser module
      • Module contents
    • immuneML.dsl.import_parsers package
      • Submodules
      • immuneML.dsl.import_parsers.ImportParser module
      • Module contents
    • immuneML.dsl.instruction_parsers package
      • Submodules
      • immuneML.dsl.instruction_parsers.DatasetExportParser module
      • immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser module
      • immuneML.dsl.instruction_parsers.LabelHelper module
      • immuneML.dsl.instruction_parsers.MLApplicationParser module
      • immuneML.dsl.instruction_parsers.SimulationParser module
      • immuneML.dsl.instruction_parsers.SubsamplingParser module
      • immuneML.dsl.instruction_parsers.TrainMLModelParser module
      • Module contents
    • immuneML.dsl.semantic_model package
      • Submodules
      • immuneML.dsl.semantic_model.MLResult module
      • immuneML.dsl.semantic_model.SemanticModel module
      • Module contents
    • immuneML.dsl.symbol_table package
      • Submodules
      • immuneML.dsl.symbol_table.SymbolTable module
      • immuneML.dsl.symbol_table.SymbolTableEntry module
      • immuneML.dsl.symbol_table.SymbolType module
      • Module contents
  • Submodules
  • immuneML.dsl.DefaultParamsLoader module
    • DefaultParamsLoader
      • DefaultParamsLoader.convert_to_snake_case()
      • DefaultParamsLoader.load()
  • immuneML.dsl.ImmuneMLParser module
    • ImmuneMLParser
      • ImmuneMLParser.check_keys()
      • ImmuneMLParser.parse()
      • ImmuneMLParser.parse_yaml_file()
  • immuneML.dsl.InstructionParser module
    • InstructionParser
      • InstructionParser.generate_docs()
      • InstructionParser.keyword
      • InstructionParser.make_docs()
      • InstructionParser.parse()
      • InstructionParser.parse_instruction()
  • immuneML.dsl.ObjectParser module
    • ObjectParser
      • ObjectParser.get_all_params()
      • ObjectParser.get_class()
      • ObjectParser.get_class_name()
      • ObjectParser.get_params()
      • ObjectParser.parse_object()
  • immuneML.dsl.OutputParser module
    • OutputParser
      • OutputParser.generate_docs()
      • OutputParser.parse()
  • immuneML.dsl.Parser module
    • Parser
      • Parser.parse()
  • Module contents
• immuneML.encodings package
  • Subpackages
    • immuneML.encodings.abundance_encoding package
      • Submodules
      • immuneML.encodings.abundance_encoding.AbundanceEncoderHelper module
      • immuneML.encodings.abundance_encoding.CompAIRRBatchIterator module
      • immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder module
      • immuneML.encodings.abundance_encoding.KmerAbundanceEncoder module
      • immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder module
      • Module contents
    • immuneML.encodings.atchley_kmer_encoding package
      • Submodules
      • immuneML.encodings.atchley_kmer_encoding.AtchleyKmerEncoder module
      • immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType module
      • immuneML.encodings.atchley_kmer_encoding.Util module
      • Module contents
    • immuneML.encodings.deeprc package
      • Submodules
      • immuneML.encodings.deeprc.DeepRCEncoder module
      • Module contents
    • immuneML.encodings.distance_encoding package
      • Submodules
      • immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder module
      • immuneML.encodings.distance_encoding.DistanceEncoder module
      • immuneML.encodings.distance_encoding.DistanceMetricType module
      • immuneML.encodings.distance_encoding.TCRdistEncoder module
      • Module contents
    • immuneML.encodings.evenness_profile package
      • Submodules
      • immuneML.encodings.evenness_profile.EvennessProfileEncoder module
      • immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder module
      • Module contents
    • immuneML.encodings.kmer_frequency package
      • Subpackages
      • Submodules
      • immuneML.encodings.kmer_frequency.KmerFreqReceptorEncoder module
      • immuneML.encodings.kmer_frequency.KmerFreqRepertoireEncoder module
      • immuneML.encodings.kmer_frequency.KmerFreqSequenceEncoder module
      • immuneML.encodings.kmer_frequency.KmerFrequencyEncoder module
      • Module contents
    • immuneML.encodings.onehot package
      • Submodules
      • immuneML.encodings.onehot.OneHotEncoder module
      • immuneML.encodings.onehot.OneHotReceptorEncoder module
      • immuneML.encodings.onehot.OneHotRepertoireEncoder module
      • immuneML.encodings.onehot.OneHotSequenceEncoder module
      • Module contents
    • immuneML.encodings.preprocessing package
      • Submodules
      • immuneML.encodings.preprocessing.FeatureScaler module
      • Module contents
    • immuneML.encodings.reference_encoding package
      • Submodules
      • 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
      • Module contents
    • immuneML.encodings.word2vec package
      • Subpackages
      • Submodules
      • immuneML.encodings.word2vec.W2VRepertoireEncoder module
      • immuneML.encodings.word2vec.W2VSequenceEncoder module
      • immuneML.encodings.word2vec.Word2VecEncoder module
      • Module contents
  • Submodules
  • immuneML.encodings.DatasetEncoder module
    • DatasetEncoder
      • DatasetEncoder.build_object()
      • DatasetEncoder.encode()
      • DatasetEncoder.get_additional_files()
      • DatasetEncoder.load_attribute()
      • DatasetEncoder.load_encoder()
      • DatasetEncoder.set_context()
      • DatasetEncoder.store()
      • DatasetEncoder.store_encoder()
  • immuneML.encodings.EncoderParams module
    • EncoderParams
      • EncoderParams.encode_labels
      • EncoderParams.get_seq_name_for_seq_object()
      • EncoderParams.get_sequence_field_name()
      • EncoderParams.label_config
      • EncoderParams.learn_model
      • EncoderParams.model
      • EncoderParams.pool_size
      • EncoderParams.region_type
      • EncoderParams.result_path
      • EncoderParams.sequence_type
  • Module contents
• immuneML.environment package
  • Submodules
  • immuneML.environment.Constants module
    • Constants
      • Constants.ALLELE_DELIMITER
      • Constants.CACHE_PATH
      • Constants.CACHE_TYPE
      • Constants.COMMENT_SIGN
      • Constants.FEATURE_DELIMITER
      • Constants.GAP_LETTER
      • Constants.GENE_DELIMITER
      • Constants.NOT_COMPUTED
      • Constants.PLOTLY_BLACK
      • Constants.SIGNAL_DELIMITER
      • Constants.STOP_CODON
      • Constants.UNKNOWN
      • Constants.VERSION
  • immuneML.environment.EnvironmentSettings module
    • EnvironmentSettings
      • EnvironmentSettings.cache_path
      • EnvironmentSettings.compairr_paths
      • EnvironmentSettings.default_analysis_path
      • EnvironmentSettings.default_params_path
      • EnvironmentSettings.get_cache_path()
      • EnvironmentSettings.get_cache_type()
      • EnvironmentSettings.get_sequence_alphabet()
      • EnvironmentSettings.get_sequence_type()
      • EnvironmentSettings.html_templates_path
      • EnvironmentSettings.low_memory
      • EnvironmentSettings.max_sequence_length
      • EnvironmentSettings.reset_cache_path()
      • EnvironmentSettings.root_path
      • EnvironmentSettings.sequence_type
      • EnvironmentSettings.set_cache_path()
      • EnvironmentSettings.set_sequence_type()
      • EnvironmentSettings.source_docs_path
      • EnvironmentSettings.specs_docs_path
      • EnvironmentSettings.tmp_cache_path
      • EnvironmentSettings.tmp_test_path
  • immuneML.environment.Label module
    • Label
      • Label.get_binary_negative_class()
      • Label.get_desc_for_storage()
      • Label.positive_class
      • Label.values
  • immuneML.environment.LabelConfiguration module
    • LabelConfiguration
      • LabelConfiguration.add_label()
      • LabelConfiguration.get_auxiliary_labels()
      • LabelConfiguration.get_label_count()
      • LabelConfiguration.get_label_object()
      • LabelConfiguration.get_label_objects()
      • LabelConfiguration.get_label_values()
      • LabelConfiguration.get_labels_by_name()
  • immuneML.environment.LabelType module
    • LabelType
      • LabelType.CLASSIFICATION
      • LabelType.REGRESSION
  • immuneML.environment.SequenceType module
    • SequenceType
      • SequenceType.AMINO_ACID
      • SequenceType.NUCLEOTIDE
  • Module contents
• immuneML.hyperparameter_optimization package
  • Subpackages
    • immuneML.hyperparameter_optimization.config package
      • Submodules
      • 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
      • Module contents
    • immuneML.hyperparameter_optimization.core package
      • Submodules
      • immuneML.hyperparameter_optimization.core.HPAssessment module
      • immuneML.hyperparameter_optimization.core.HPSelection module
      • immuneML.hyperparameter_optimization.core.HPUtil module
      • Module contents
    • immuneML.hyperparameter_optimization.states package
      • Submodules
      • immuneML.hyperparameter_optimization.states.HPAssessmentState module
      • immuneML.hyperparameter_optimization.states.HPItem module
      • immuneML.hyperparameter_optimization.states.HPLabelState module
      • immuneML.hyperparameter_optimization.states.HPSelectionState module
      • immuneML.hyperparameter_optimization.states.TrainMLModelState module
      • Module contents
    • immuneML.hyperparameter_optimization.strategy package
      • Submodules
      • immuneML.hyperparameter_optimization.strategy.GridSearch module
      • immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy module
      • Module contents
  • Submodules
  • immuneML.hyperparameter_optimization.HPSetting module
    • HPSetting
      • HPSetting.get_key()
  • immuneML.hyperparameter_optimization.HPSettingResult module
    • HPSettingResult
  • Module contents
• immuneML.ml_methods package
  • Subpackages
    • immuneML.ml_methods.pytorch_implementations package
      • Submodules
      • immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression module
      • immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN module
      • Module contents
    • immuneML.ml_methods.util package
      • Submodules
      • immuneML.ml_methods.util.Util module
      • Module contents
  • Submodules
  • immuneML.ml_methods.AtchleyKmerMILClassifier module
  • immuneML.ml_methods.DeepRC module
  • immuneML.ml_methods.KNN module
  • immuneML.ml_methods.LogisticRegression module
  • immuneML.ml_methods.MLMethod module
  • immuneML.ml_methods.PrecomputedKNN module
  • immuneML.ml_methods.ProbabilisticBinaryClassifier module
  • immuneML.ml_methods.RandomForestClassifier module
  • immuneML.ml_methods.ReceptorCNN module
  • immuneML.ml_methods.SVC module
  • immuneML.ml_methods.SVM module
  • immuneML.ml_methods.SklearnMethod module
  • immuneML.ml_methods.TCRdistClassifier module
  • Module contents
• immuneML.ml_metrics package
  • Submodules
  • immuneML.ml_metrics.Metric module
  • immuneML.ml_metrics.MetricUtil module
    • MetricUtil
      • MetricUtil.get_metric_fn()
      • MetricUtil.score_for_metric()
  • immuneML.ml_metrics.ml_metrics module
    • f1_score_macro()
    • f1_score_micro()
    • f1_score_weighted()
    • roc_auc_score()
  • Module contents
• immuneML.pairwise_repertoire_comparison package
  • Submodules
  • immuneML.pairwise_repertoire_comparison.ComparisonData module
    • ComparisonData
      • ComparisonData.add_items_for_repertoire()
      • ComparisonData.filter_existing_items()
      • ComparisonData.get_batch()
      • ComparisonData.get_batches()
      • ComparisonData.get_item_names()
      • ComparisonData.get_item_vector()
      • ComparisonData.get_item_vectors()
      • ComparisonData.get_repertoire_vector()
      • ComparisonData.get_repertoire_vectors()
      • ComparisonData.get_tmp_batches()
      • ComparisonData.load_tmp_batch()
      • ComparisonData.merge_tmp_batches_to_matrix()
      • ComparisonData.process_dataset()
      • ComparisonData.process_repertoire()
      • ComparisonData.set_iteration_repertoire_ids()
      • ComparisonData.store_tmp_batch()
  • immuneML.pairwise_repertoire_comparison.ComparisonDataBatch module
    • ComparisonDataBatch
      • ComparisonDataBatch.get_items()
      • ComparisonDataBatch.get_matrix()
      • ComparisonDataBatch.identifier
      • ComparisonDataBatch.items
      • ComparisonDataBatch.load()
      • ComparisonDataBatch.matrix
      • ComparisonDataBatch.path
      • ComparisonDataBatch.repertoire_index_mapping
      • ComparisonDataBatch.store()
  • immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison module
    • PairwiseRepertoireComparison
      • PairwiseRepertoireComparison.compare()
      • PairwiseRepertoireComparison.compare_repertoires()
      • PairwiseRepertoireComparison.create_comparison_data()
      • PairwiseRepertoireComparison.memo_by_params()
      • PairwiseRepertoireComparison.prepare_caching_params()
      • PairwiseRepertoireComparison.prepare_paralellization_arguments()
  • Module contents
• immuneML.preprocessing package
  • Subpackages
    • immuneML.preprocessing.filters package
      • Submodules
      • immuneML.preprocessing.filters.ChainRepertoireFilter module
      • immuneML.preprocessing.filters.ClonesPerRepertoireFilter module
      • immuneML.preprocessing.filters.CountAggregationFunction module
      • immuneML.preprocessing.filters.CountPerSequenceFilter module
      • immuneML.preprocessing.filters.DuplicateSequenceFilter module
      • immuneML.preprocessing.filters.Filter module
      • immuneML.preprocessing.filters.MetadataRepertoireFilter module
      • immuneML.preprocessing.filters.SequenceLengthFilter module
      • Module contents
  • Submodules
  • immuneML.preprocessing.Preprocessor module
    • Preprocessor
      • Preprocessor.check_dataset_type()
      • Preprocessor.keeps_example_count()
      • Preprocessor.process_dataset()
  • immuneML.preprocessing.ReferenceSequenceAnnotator module
    • ReferenceSequenceAnnotator
      • ReferenceSequenceAnnotator.build_object()
      • ReferenceSequenceAnnotator.process_dataset()
  • immuneML.preprocessing.SubjectRepertoireCollector module
    • SubjectRepertoireCollector
      • SubjectRepertoireCollector.keeps_example_count()
      • SubjectRepertoireCollector.process_dataset()
  • Module contents
• immuneML.presentation package
  • Subpackages
    • immuneML.presentation.html package
      • Submodules
      • immuneML.presentation.html.DatasetExportHTMLBuilder module
      • immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder module
      • immuneML.presentation.html.HPHTMLBuilder module
      • immuneML.presentation.html.HTMLBuilder module
      • immuneML.presentation.html.MLApplicationHTMLBuilder module
      • immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder module
      • immuneML.presentation.html.SimulationHTMLBuilder module
      • immuneML.presentation.html.SubsamplingHTMLBuilder module
      • immuneML.presentation.html.Util module
      • Module contents
  • Submodules
  • immuneML.presentation.InstructionPresentation module
    • InstructionPresentation
      • InstructionPresentation.instruction_class
      • InstructionPresentation.instruction_name
      • InstructionPresentation.path
  • immuneML.presentation.PresentationFactory module
    • PresentationFactory
      • PresentationFactory.make_presentation_builder()
  • immuneML.presentation.PresentationFormat module
    • PresentationFormat
      • PresentationFormat.HTML
  • immuneML.presentation.TemplateParser module
    • TemplateParser
      • TemplateParser.parse()
  • Module contents
• immuneML.reports package
  • Subpackages
    • immuneML.reports.data_reports package
      • Submodules
      • immuneML.reports.data_reports.AminoAcidFrequencyDistribution module
      • immuneML.reports.data_reports.CytoscapeNetworkExporter module
      • immuneML.reports.data_reports.DataReport module
      • immuneML.reports.data_reports.GLIPH2Exporter module
      • immuneML.reports.data_reports.ReceptorDatasetOverview module
      • immuneML.reports.data_reports.RecoveredSignificantFeatures module
      • immuneML.reports.data_reports.RepertoireClonotypeSummary module
      • immuneML.reports.data_reports.SequenceLengthDistribution module
      • immuneML.reports.data_reports.SequencesWithSignificantKmers module
      • immuneML.reports.data_reports.SignificantFeatures module
      • immuneML.reports.data_reports.SignificantKmerPositions module
      • immuneML.reports.data_reports.SimpleDatasetOverview module
      • Module contents
    • immuneML.reports.encoding_reports package
      • Submodules
      • 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
      • Module contents
    • immuneML.reports.ml_reports package
      • Submodules
      • immuneML.reports.ml_reports.CoefficientPlottingSetting module
      • immuneML.reports.ml_reports.CoefficientPlottingSettingList module
      • immuneML.reports.ml_reports.Coefficients module
      • immuneML.reports.ml_reports.ConfounderAnalysis module
      • immuneML.reports.ml_reports.DeepRCMotifDiscovery module
      • immuneML.reports.ml_reports.KernelSequenceLogo module
      • immuneML.reports.ml_reports.MLReport module
      • immuneML.reports.ml_reports.MotifSeedRecovery module
      • immuneML.reports.ml_reports.ROCCurve module
      • immuneML.reports.ml_reports.SequenceAssociationLikelihood module
      • immuneML.reports.ml_reports.TCRdistMotifDiscovery module
      • immuneML.reports.ml_reports.TrainingPerformance module
      • Module contents
    • immuneML.reports.multi_dataset_reports package
      • Submodules
      • immuneML.reports.multi_dataset_reports.DiseaseAssociatedSequenceOverlap module
      • immuneML.reports.multi_dataset_reports.MultiDatasetReport module
      • immuneML.reports.multi_dataset_reports.PerformanceOverview module
      • Module contents
    • immuneML.reports.train_ml_model_reports package
      • Submodules
      • immuneML.reports.train_ml_model_reports.CVFeaturePerformance module
      • immuneML.reports.train_ml_model_reports.DiseaseAssociatedSequenceCVOverlap module
      • immuneML.reports.train_ml_model_reports.MLSettingsPerformance module
      • immuneML.reports.train_ml_model_reports.ROCCurveSummary module
      • immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap module
      • immuneML.reports.train_ml_model_reports.TrainMLModelReport module
      • Module contents
  • Submodules
  • immuneML.reports.PlotlyUtil module
    • PlotlyUtil
      • PlotlyUtil.add_single_axis_labels()
      • PlotlyUtil.get_amino_acid_color_map()
  • immuneML.reports.Report module
    • Report
      • Report.build_object()
      • Report.check_prerequisites()
      • Report.generate_report()
      • Report.set_context()
  • immuneML.reports.ReportOutput module
    • ReportOutput
  • immuneML.reports.ReportResult module
    • ReportResult
      • ReportResult.info
      • ReportResult.name
      • ReportResult.output_figures
      • ReportResult.output_tables
      • ReportResult.output_text
  • immuneML.reports.ReportUtil module
    • ReportUtil
      • ReportUtil.run_ML_reports()
      • ReportUtil.run_data_reports()
      • ReportUtil.run_encoding_reports()
      • ReportUtil.update_split_by_label_kwargs()
  • Module contents
• immuneML.simulation package
  • Subpackages
    • immuneML.simulation.dataset_generation package
      • Submodules
      • immuneML.simulation.dataset_generation.RandomDatasetGenerator module
      • Module contents
    • immuneML.simulation.implants package
      • Submodules
      • immuneML.simulation.implants.ImplantAnnotation module
      • immuneML.simulation.implants.Motif module
      • immuneML.simulation.implants.MotifInstance module
      • immuneML.simulation.implants.Signal module
      • Module contents
    • immuneML.simulation.motif_instantiation_strategy package
      • Submodules
      • immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation module
      • immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy module
      • Module contents
    • immuneML.simulation.sequence_implanting package
      • Submodules
      • immuneML.simulation.sequence_implanting.GappedMotifImplanting module
      • immuneML.simulation.sequence_implanting.SequenceImplantingStrategy module
      • Module contents
    • immuneML.simulation.signal_implanting_strategy package
      • Submodules
      • immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting module
      • immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting module
      • immuneML.simulation.signal_implanting_strategy.ImplantingComputation module
      • immuneML.simulation.signal_implanting_strategy.ReceptorImplanting module
      • immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy module
      • Module contents
  • Submodules
  • immuneML.simulation.Implanting module
  • immuneML.simulation.Simulation module
  • immuneML.simulation.SimulationState module
  • Module contents
• immuneML.util package
  • Submodules
  • immuneML.util.AdaptiveImportHelper module
    • AdaptiveImportHelper
      • AdaptiveImportHelper.parse_adaptive_germline_to_imgt()
      • AdaptiveImportHelper.parse_germline()
      • AdaptiveImportHelper.preprocess_dataframe()
    • is_valid_sequence_str()
    • make_gene_call_from_gene_and_allele()
    • parse_allele()
    • parse_gene_column()
    • replace_nans_with_empty_str()
    • set_locus_column()
  • immuneML.util.CompAIRRHelper module
    • CompAIRRHelper
      • CompAIRRHelper.check_compairr_path()
      • CompAIRRHelper.determine_compairr_path()
      • CompAIRRHelper.get_cmd_args()
      • CompAIRRHelper.get_repertoire_contents()
      • CompAIRRHelper.process_compairr_output_file()
      • CompAIRRHelper.read_compairr_output_file()
      • CompAIRRHelper.verify_compairr_output_path()
      • CompAIRRHelper.write_repertoire_file()
      • CompAIRRHelper.write_sequences_file()
  • immuneML.util.CompAIRRParams module
    • CompAIRRParams
      • CompAIRRParams.compairr_path
      • CompAIRRParams.differences
      • CompAIRRParams.do_repertoire_overlap
      • CompAIRRParams.do_sequence_matching
      • CompAIRRParams.ignore_counts
      • CompAIRRParams.ignore_genes
      • CompAIRRParams.indels
      • CompAIRRParams.is_cdr3
      • CompAIRRParams.keep_compairr_input
      • CompAIRRParams.log_filename
      • CompAIRRParams.output_filename
      • CompAIRRParams.output_pairs
      • CompAIRRParams.pairs_filename
      • CompAIRRParams.threads
  • immuneML.util.DistanceMetrics module
    • jaccard()
    • morisita_horn()
  • immuneML.util.DocEnumHelper module
    • DocEnumHelper
      • DocEnumHelper.get_enum_names()
      • DocEnumHelper.get_enum_names_and_values()
  • immuneML.util.EncoderHelper module
    • EncoderHelper
      • EncoderHelper.build_comparison_data()
      • EncoderHelper.build_comparison_params()
      • EncoderHelper.check_dataset_type_available_in_mapping()
      • EncoderHelper.check_positive_class_labels()
      • EncoderHelper.encode_dataset_labels()
      • EncoderHelper.encode_element_dataset_labels()
      • EncoderHelper.encode_repertoire_dataset_labels()
      • EncoderHelper.get_current_dataset()
      • EncoderHelper.get_example_weights_by_identifiers()
      • EncoderHelper.get_single_label_name_from_config()
      • EncoderHelper.prepare_training_ids()
      • EncoderHelper.sync_encoder_with_cache()
  • immuneML.util.FilenameHandler module
    • FilenameHandler
      • FilenameHandler.get_dataset_name()
      • FilenameHandler.get_filename()
      • FilenameHandler.get_model_name()
  • immuneML.util.ImportHelper module
    • ImportHelper
      • ImportHelper.DATASET_FORMAT
      • ImportHelper.INVALID_COLNAME_CHARS
      • ImportHelper.add_cdr3_from_junction()
      • ImportHelper.add_default_fields_for_airr_seq_set()
      • ImportHelper.drop_empty_sequences()
      • ImportHelper.drop_illegal_character_sequences()
      • ImportHelper.extract_locus_from_data()
      • ImportHelper.extract_sequence_dataset_params()
      • ImportHelper.filter_illegal_receptors()
      • ImportHelper.filter_illegal_sequences()
      • ImportHelper.get_receptor_filter_sort_kwargs()
      • ImportHelper.get_repertoire_filename_from_metadata_row()
      • ImportHelper.get_sequence_filenames()
      • ImportHelper.get_standardized_name()
      • ImportHelper.is_illegal_sequence()
      • ImportHelper.make_new_metadata_file()
      • ImportHelper.parse_sequence_dataframe()
      • ImportHelper.standardize_column_names()
      • ImportHelper.standardize_none_values()
  • immuneML.util.KmerHelper module
    • KmerHelper
      • KmerHelper.create_IMGT_gapped_kmers_from_sequence()
      • KmerHelper.create_IMGT_kmers_from_sequence()
      • KmerHelper.create_IMGT_kmers_from_string()
      • KmerHelper.create_all_kmers()
      • KmerHelper.create_gapped_kmers_from_sequence()
      • KmerHelper.create_gapped_kmers_from_string()
      • KmerHelper.create_kmers_from_sequence()
      • KmerHelper.create_kmers_from_string()
      • KmerHelper.create_kmers_within_HD()
      • KmerHelper.create_sentences_from_repertoire()
  • immuneML.util.Logger module
    • log()
    • print_log()
  • immuneML.util.NameBuilder module
    • NameBuilder
      • NameBuilder.build_name_from_dict()
  • immuneML.util.NumpyHelper module
    • NumpyHelper
      • NumpyHelper.SIMPLE_TYPES
      • NumpyHelper.get_numpy_representation()
      • NumpyHelper.group_structured_array_by()
      • NumpyHelper.is_nan_or_empty()
      • NumpyHelper.is_simple_type()
  • immuneML.util.ParameterValidator module
    • ParameterValidator
      • ParameterValidator.assert_all_in_valid_list()
      • ParameterValidator.assert_all_type_and_value()
      • ParameterValidator.assert_any_value_present()
      • ParameterValidator.assert_in_valid_list()
      • ParameterValidator.assert_keys()
      • ParameterValidator.assert_keys_present()
      • ParameterValidator.assert_region_type()
      • ParameterValidator.assert_sequence_type()
      • ParameterValidator.assert_type_and_value()
      • ParameterValidator.assert_valid_tabular_file()
  • immuneML.util.PathBuilder module
    • PathBuilder
      • PathBuilder.build()
      • PathBuilder.remove_old_and_build()
  • immuneML.util.PositionHelper module
    • PositionHelper
      • PositionHelper.MAX_CDR3_LEN
      • PositionHelper.MIDPOINT_CDR3_LEN
      • PositionHelper.MIN_CDR3_LEN
      • PositionHelper.gen_imgt_positions_from_cdr3_length()
      • PositionHelper.gen_imgt_positions_from_junction_length()
      • PositionHelper.gen_imgt_positions_from_length()
      • PositionHelper.gen_imgt_positions_from_sequence()
      • PositionHelper.get_allowed_positions_for_annotation()
      • PositionHelper.get_imgt_position_weights_for_annotation()
      • PositionHelper.get_imgt_position_weights_for_implanting()
  • immuneML.util.ReadsType module
    • ReadsType
      • ReadsType.ALL
      • ReadsType.UNIQUE
  • immuneML.util.ReflectionHandler module
    • ReflectionHandler
      • ReflectionHandler.all_direct_subclasses()
      • ReflectionHandler.all_nonabstract_subclass_basic_names()
      • ReflectionHandler.all_nonabstract_subclasses()
      • ReflectionHandler.all_subclasses()
      • ReflectionHandler.discover_classes_by_partial_name()
      • ReflectionHandler.exists()
      • ReflectionHandler.get_class_by_name()
      • ReflectionHandler.get_class_from_path()
      • ReflectionHandler.get_classes_by_partial_name()
      • ReflectionHandler.import_function()
      • ReflectionHandler.import_module()
      • ReflectionHandler.is_installed()
  • immuneML.util.RepertoireBuilder module
    • RepertoireBuilder
      • RepertoireBuilder.build()
      • RepertoireBuilder.build_dataset()
  • immuneML.util.SequenceAnalysisHelper module
    • SequenceAnalysisHelper
      • SequenceAnalysisHelper.compute_overlap_matrix()
  • immuneML.util.SignificantFeaturesHelper module
    • SignificantFeaturesHelper
      • SignificantFeaturesHelper.load_sequences()
      • SignificantFeaturesHelper.parse_parameters()
      • SignificantFeaturesHelper.parse_sequences_path()
  • immuneML.util.StringHelper module
    • StringHelper
      • StringHelper.camel_case_to_word_string()
      • StringHelper.camel_case_to_words()
      • StringHelper.pad_sequence_in_the_middle()
  • immuneML.util.TCRdistHelper module
    • TCRdistHelper
      • TCRdistHelper.add_default_allele_to_v_gene()
      • TCRdistHelper.compute_tcr_dist()
      • TCRdistHelper.prepare_tcr_dist_dataframe()
  • Module contents
• immuneML.workflows package
  • Subpackages
    • immuneML.workflows.instructions package
      • Subpackages
      • Submodules
      • immuneML.workflows.instructions.Instruction module
      • immuneML.workflows.instructions.MLProcess module
      • immuneML.workflows.instructions.SimulationInstruction module
      • immuneML.workflows.instructions.TrainMLModelInstruction module
      • immuneML.workflows.instructions.quickstart module
      • Module contents
    • immuneML.workflows.steps package
      • Subpackages
      • Submodules
      • immuneML.workflows.steps.DataEncoder module
      • immuneML.workflows.steps.DataEncoderParams module
      • immuneML.workflows.steps.MLMethodAssessment module
      • immuneML.workflows.steps.MLMethodAssessmentParams module
      • immuneML.workflows.steps.MLMethodTrainer module
      • immuneML.workflows.steps.MLMethodTrainerParams module
      • immuneML.workflows.steps.SignalImplanter module
      • immuneML.workflows.steps.Step module
      • immuneML.workflows.steps.StepParams module
      • Module contents
  • Module contents

Module contents