Python Module Index

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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.build_dataset_yaml
    immuneML.api.galaxy.build_yaml_from_arguments
    immuneML.api.galaxy.DatasetGenerationTool
    immuneML.api.galaxy.DataSimulationTool
    immuneML.api.galaxy.GalaxyMLApplicationTool
    immuneML.api.galaxy.GalaxySimulationTool
    immuneML.api.galaxy.GalaxyTool
    immuneML.api.galaxy.GalaxyTrainMLModel
    immuneML.api.galaxy.GalaxyYamlTool
    immuneML.api.galaxy.RepertoireClassificationTool
    immuneML.api.galaxy.Util
    immuneML.app
    immuneML.app.ImmuneMLApp
    immuneML.caching
    immuneML.caching.CacheHandler
    immuneML.caching.CacheObjectType
    immuneML.caching.CacheType
    immuneML.data_model
    immuneML.data_model.cell
    immuneML.data_model.cell.Cell
    immuneML.data_model.cell.CellList
    immuneML.data_model.dataset
    immuneML.data_model.dataset.Dataset
    immuneML.data_model.dataset.ElementDataset
    immuneML.data_model.dataset.ReceptorDataset
    immuneML.data_model.dataset.RepertoireDataset
    immuneML.data_model.dataset.SequenceDataset
    immuneML.data_model.DatasetItem
    immuneML.data_model.encoded_data
    immuneML.data_model.encoded_data.EncodedData
    immuneML.data_model.receptor
    immuneML.data_model.receptor.BCKReceptor
    immuneML.data_model.receptor.BCReceptor
    immuneML.data_model.receptor.ChainPair
    immuneML.data_model.receptor.ElementGenerator
    immuneML.data_model.receptor.Receptor
    immuneML.data_model.receptor.receptor_sequence
    immuneML.data_model.receptor.receptor_sequence.Chain
    immuneML.data_model.receptor.receptor_sequence.ReceptorSequence
    immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation
    immuneML.data_model.receptor.receptor_sequence.SequenceFrameType
    immuneML.data_model.receptor.receptor_sequence.SequenceMetadata
    immuneML.data_model.receptor.ReceptorBuilder
    immuneML.data_model.receptor.RegionType
    immuneML.data_model.receptor.TCABReceptor
    immuneML.data_model.receptor.TCGDReceptor
    immuneML.data_model.repertoire
    immuneML.data_model.repertoire.Repertoire
    immuneML.dev_util
    immuneML.dev_util.util
    immuneML.dsl
    immuneML.dsl.DefaultParamsLoader
    immuneML.dsl.definition_parsers
    immuneML.dsl.definition_parsers.DefinitionParser
    immuneML.dsl.definition_parsers.DefinitionParserOutput
    immuneML.dsl.definition_parsers.EncodingParser
    immuneML.dsl.definition_parsers.MLParser
    immuneML.dsl.definition_parsers.MotifParser
    immuneML.dsl.definition_parsers.PreprocessingParser
    immuneML.dsl.definition_parsers.ReportParser
    immuneML.dsl.definition_parsers.SignalParser
    immuneML.dsl.definition_parsers.SimulationParser
    immuneML.dsl.ImmuneMLParser
    immuneML.dsl.import_parsers
    immuneML.dsl.import_parsers.ImportParser
    immuneML.dsl.instruction_parsers
    immuneML.dsl.instruction_parsers.DatasetExportParser
    immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser
    immuneML.dsl.instruction_parsers.LabelHelper
    immuneML.dsl.instruction_parsers.MLApplicationParser
    immuneML.dsl.instruction_parsers.SimulationParser
    immuneML.dsl.instruction_parsers.SubsamplingParser
    immuneML.dsl.instruction_parsers.TrainMLModelParser
    immuneML.dsl.InstructionParser
    immuneML.dsl.ObjectParser
    immuneML.dsl.OutputParser
    immuneML.dsl.Parser
    immuneML.dsl.semantic_model
    immuneML.dsl.semantic_model.MLResult
    immuneML.dsl.semantic_model.SemanticModel
    immuneML.dsl.symbol_table
    immuneML.dsl.symbol_table.SymbolTable
    immuneML.dsl.symbol_table.SymbolTableEntry
    immuneML.dsl.symbol_table.SymbolType
    immuneML.encodings
    immuneML.encodings.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_export.ImmuneMLExporter
    immuneML.IO.dataset_import
    immuneML.IO.dataset_import.AIRRImport
    immuneML.IO.dataset_import.DataImport
    immuneML.IO.dataset_import.DatasetImportParams
    immuneML.IO.dataset_import.GenericImport
    immuneML.IO.dataset_import.IGoRImport
    immuneML.IO.dataset_import.ImmuneMLImport
    immuneML.IO.dataset_import.ImmunoSEQRearrangementImport
    immuneML.IO.dataset_import.ImmunoSEQSampleImport
    immuneML.IO.dataset_import.IReceptorImport
    immuneML.IO.dataset_import.MiXCRImport
    immuneML.IO.dataset_import.OLGAImport
    immuneML.IO.dataset_import.RandomReceptorDatasetImport
    immuneML.IO.dataset_import.RandomRepertoireDatasetImport
    immuneML.IO.dataset_import.RandomSequenceDatasetImport
    immuneML.IO.dataset_import.SingleLineReceptorImport
    immuneML.IO.dataset_import.TenxGenomicsImport
    immuneML.IO.dataset_import.VDJdbImport
    immuneML.IO.ml_method
    immuneML.IO.ml_method.MLExporter
    immuneML.IO.ml_method.MLImport
    immuneML.IO.ml_method.MLMethodConfiguration
    immuneML.IO.ml_method.UtilIO
    immuneML.ml_methods
    immuneML.ml_methods.AtchleyKmerMILClassifier
    immuneML.ml_methods.DeepRC
    immuneML.ml_methods.KNN
    immuneML.ml_methods.LogisticRegression
    immuneML.ml_methods.MLMethod
    immuneML.ml_methods.PrecomputedKNN
    immuneML.ml_methods.ProbabilisticBinaryClassifier
    immuneML.ml_methods.pytorch_implementations
    immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression
    immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN
    immuneML.ml_methods.RandomForestClassifier
    immuneML.ml_methods.ReceptorCNN
    immuneML.ml_methods.SklearnMethod
    immuneML.ml_methods.SVC
    immuneML.ml_methods.SVM
    immuneML.ml_methods.TCRdistClassifier
    immuneML.ml_methods.util
    immuneML.ml_methods.util.Util
    immuneML.ml_metrics
    immuneML.ml_metrics.Metric
    immuneML.ml_metrics.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.SimulationHTMLBuilder
    immuneML.presentation.html.SubsamplingHTMLBuilder
    immuneML.presentation.html.Util
    immuneML.presentation.InstructionPresentation
    immuneML.presentation.PresentationFactory
    immuneML.presentation.PresentationFormat
    immuneML.presentation.TemplateParser
    immuneML.reports
    immuneML.reports.data_reports
    immuneML.reports.data_reports.AminoAcidFrequencyDistribution
    immuneML.reports.data_reports.CytoscapeNetworkExporter
    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.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.Implanting
    immuneML.simulation.implants
    immuneML.simulation.implants.ImplantAnnotation
    immuneML.simulation.implants.Motif
    immuneML.simulation.implants.MotifInstance
    immuneML.simulation.implants.Signal
    immuneML.simulation.motif_instantiation_strategy
    immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation
    immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy
    immuneML.simulation.sequence_implanting
    immuneML.simulation.sequence_implanting.GappedMotifImplanting
    immuneML.simulation.sequence_implanting.SequenceImplantingStrategy
    immuneML.simulation.signal_implanting_strategy
    immuneML.simulation.signal_implanting_strategy.FullSequenceImplanting
    immuneML.simulation.signal_implanting_strategy.HealthySequenceImplanting
    immuneML.simulation.signal_implanting_strategy.ImplantingComputation
    immuneML.simulation.signal_implanting_strategy.ReceptorImplanting
    immuneML.simulation.signal_implanting_strategy.SignalImplantingStrategy
    immuneML.simulation.Simulation
    immuneML.simulation.SimulationState
    immuneML.util
    immuneML.util.AdaptiveImportHelper
    immuneML.util.CompAIRRHelper
    immuneML.util.CompAIRRParams
    immuneML.util.DistanceMetrics
    immuneML.util.DocEnumHelper
    immuneML.util.EncoderHelper
    immuneML.util.FilenameHandler
    immuneML.util.ImportHelper
    immuneML.util.KmerHelper
    immuneML.util.Logger
    immuneML.util.NameBuilder
    immuneML.util.NumpyHelper
    immuneML.util.ParameterValidator
    immuneML.util.PathBuilder
    immuneML.util.PositionHelper
    immuneML.util.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.ml_model_application
    immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction
    immuneML.workflows.instructions.ml_model_application.MLApplicationState
    immuneML.workflows.instructions.MLProcess
    immuneML.workflows.instructions.quickstart
    immuneML.workflows.instructions.SimulationInstruction
    immuneML.workflows.instructions.subsampling
    immuneML.workflows.instructions.subsampling.SubsamplingInstruction
    immuneML.workflows.instructions.subsampling.SubsamplingState
    immuneML.workflows.instructions.TrainMLModelInstruction
    immuneML.workflows.steps
    immuneML.workflows.steps.data_splitter
    immuneML.workflows.steps.data_splitter.DataSplitter
    immuneML.workflows.steps.data_splitter.DataSplitterParams
    immuneML.workflows.steps.data_splitter.LeaveOneOutSplitter
    immuneML.workflows.steps.data_splitter.ManualSplitter
    immuneML.workflows.steps.data_splitter.Util
    immuneML.workflows.steps.DataEncoder
    immuneML.workflows.steps.DataEncoderParams
    immuneML.workflows.steps.MLMethodAssessment
    immuneML.workflows.steps.MLMethodAssessmentParams
    immuneML.workflows.steps.MLMethodTrainer
    immuneML.workflows.steps.MLMethodTrainerParams
    immuneML.workflows.steps.SignalImplanter
    immuneML.workflows.steps.Step
    immuneML.workflows.steps.StepParams