Python Module Index


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