immuneML package¶
Subpackages¶
- immuneML.IO package
- Subpackages
- immuneML.IO.dataset_export package
- 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.IRISImport module
- immuneML.IO.dataset_import.IRISImportParams module
- immuneML.IO.dataset_import.IRISSequenceImport module
- immuneML.IO.dataset_import.IReceptorImport 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.PickleImport 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
- Module contents
- Subpackages
- 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
- immuneML.analysis.entropy_calculations package
- immuneML.analysis.similarities package
- immuneML.analysis.criteria_matches package
- Submodules
- immuneML.analysis.AxisType module
- immuneML.analysis.SequenceMatcher module
- Module contents
- Subpackages
- immuneML.api package
- Subpackages
- immuneML.api.aggregated_runs package
- 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
- Module contents
- Subpackages
- immuneML.app package
- immuneML.caching package
- immuneML.data_model package
- Subpackages
- immuneML.data_model.cell package
- immuneML.data_model.dataset package
- immuneML.data_model.encoded_data package
- 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.DatasetItem module
- Module contents
- Subpackages
- immuneML.dev_util package
- 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
- immuneML.dsl.instruction_parsers package
- Submodules
- immuneML.dsl.instruction_parsers.DatasetExportParser module
- immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser 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
- immuneML.dsl.symbol_table package
- immuneML.dsl.definition_parsers package
- Submodules
- immuneML.dsl.DefaultParamsLoader module
- immuneML.dsl.ImmuneMLParser module
- immuneML.dsl.InstructionParser module
- immuneML.dsl.ObjectParser module
- immuneML.dsl.OutputParser module
- immuneML.dsl.Parser module
- Module contents
- Subpackages
- immuneML.encodings package
- Subpackages
- immuneML.encodings.atchley_kmer_encoding package
- immuneML.encodings.deeprc package
- immuneML.encodings.distance_encoding package
- immuneML.encodings.evenness_profile package
- immuneML.encodings.filtered_sequence_encoding package
- 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
- immuneML.encodings.kmer_frequency.ReadsType module
- Module contents
- immuneML.encodings.onehot package
- immuneML.encodings.preprocessing package
- immuneML.encodings.reference_encoding package
- Submodules
- immuneML.encodings.reference_encoding.MatchedReceptorsEncoder module
- immuneML.encodings.reference_encoding.MatchedReceptorsRepertoireEncoder module
- immuneML.encodings.reference_encoding.MatchedReferenceUtil module
- immuneML.encodings.reference_encoding.MatchedRegexEncoder module
- immuneML.encodings.reference_encoding.MatchedRegexRepertoireEncoder module
- immuneML.encodings.reference_encoding.MatchedSequencesEncoder module
- immuneML.encodings.reference_encoding.MatchedSequencesRepertoireEncoder module
- immuneML.encodings.reference_encoding.SequenceMatchingSummaryType module
- Module contents
- immuneML.encodings.word2vec package
- Submodules
- immuneML.encodings.DatasetEncoder module
- immuneML.encodings.EncoderParams module
- Module contents
- Subpackages
- immuneML.environment package
- Submodules
- immuneML.environment.Constants module
- immuneML.environment.EnvironmentSettings module
- immuneML.environment.Label module
- immuneML.environment.LabelConfiguration module
- immuneML.environment.LabelType module
- immuneML.environment.Metric module
- immuneML.environment.SequenceType module
- 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
- 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
- immuneML.hyperparameter_optimization.config package
- Submodules
- immuneML.hyperparameter_optimization.HPSetting module
- immuneML.hyperparameter_optimization.HPSettingResult module
- Module contents
- Subpackages
- immuneML.ml_methods package
- Subpackages
- 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.ProbabilisticBinaryClassifier module
- immuneML.ml_methods.RandomForestClassifier module
- immuneML.ml_methods.ReceptorCNN module
- immuneML.ml_methods.SVM module
- immuneML.ml_methods.SklearnMethod module
- immuneML.ml_methods.TCRdistClassifier module
- Module contents
- immuneML.ml_metrics package
- immuneML.pairwise_repertoire_comparison package
- 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
- Module contents
- immuneML.preprocessing.filters package
- Submodules
- immuneML.preprocessing.Preprocessor module
- immuneML.preprocessing.SubjectRepertoireCollector module
- Module contents
- Subpackages
- 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
- immuneML.presentation.html package
- Submodules
- immuneML.presentation.InstructionPresentation module
- immuneML.presentation.PresentationFactory module
- immuneML.presentation.PresentationFormat module
- immuneML.presentation.TemplateParser module
- Module contents
- Subpackages
- immuneML.reports package
- Subpackages
- immuneML.reports.data_reports package
- Submodules
- immuneML.reports.data_reports.CytoscapeNetworkExporter module
- immuneML.reports.data_reports.DataReport module
- immuneML.reports.data_reports.GLIPH2Exporter module
- immuneML.reports.data_reports.ReceptorDatasetOverview module
- immuneML.reports.data_reports.SequenceLengthDistribution module
- Module contents
- immuneML.reports.encoding_reports package
- Submodules
- immuneML.reports.encoding_reports.DesignMatrixExporter module
- immuneML.reports.encoding_reports.EncodingReport module
- immuneML.reports.encoding_reports.FeatureDistribution 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.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
- 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.MLSubseqPerformance 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
- immuneML.reports.data_reports package
- Submodules
- immuneML.reports.PlotlyUtil module
- immuneML.reports.Report module
- immuneML.reports.ReportOutput module
- immuneML.reports.ReportResult module
- immuneML.reports.ReportUtil module
- Module contents
- Subpackages
- immuneML.simulation package
- Subpackages
- immuneML.simulation.dataset_generation package
- immuneML.simulation.implants package
- immuneML.simulation.motif_instantiation_strategy package
- immuneML.simulation.sequence_implanting package
- 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
- Subpackages
- immuneML.util package
- Submodules
- immuneML.util.AdaptiveImportHelper module
- immuneML.util.DistanceMetrics module
- immuneML.util.DocEnumHelper module
- immuneML.util.EncoderHelper module
- immuneML.util.FilenameHandler module
- immuneML.util.ImportHelper module
- immuneML.util.KmerHelper module
- immuneML.util.Logger module
- immuneML.util.NameBuilder module
- immuneML.util.NumpyHelper module
- immuneML.util.ParameterValidator module
- immuneML.util.PathBuilder module
- immuneML.util.PositionHelper module
- immuneML.util.ReflectionHandler module
- immuneML.util.RepertoireBuilder module
- immuneML.util.SequenceAnalysisHelper module
- immuneML.util.StringHelper module
- immuneML.util.TCRdistHelper module
- 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
- immuneML.workflows.instructions package
- Module contents
- Subpackages