All modules for which code is available

• immuneML.IO.dataset_export.AIRRExporter
• immuneML.IO.dataset_export.DataExporter
• immuneML.IO.dataset_export.ImmuneMLExporter
• 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.IReceptorImport
• immuneML.IO.dataset_import.ImmuneMLImport
• immuneML.IO.dataset_import.ImmunoSEQRearrangementImport
• immuneML.IO.dataset_import.ImmunoSEQSampleImport
• 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.MLExporter
• immuneML.IO.ml_method.MLImport
• immuneML.IO.ml_method.MLMethodConfiguration
• immuneML.IO.ml_method.UtilIO
• immuneML.analysis.AxisType
• immuneML.analysis.SequenceMatcher
• 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.DataReshaper
• immuneML.analysis.data_manipulation.NormalizationType
• immuneML.analysis.data_manipulation.ReductionMethod
• immuneML.analysis.entropy_calculations.EntropyCalculator
• immuneML.analysis.similarities.SimilarityMeasureType
• immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool
• immuneML.api.api_encoding
• immuneML.api.galaxy.DataSimulationTool
• immuneML.api.galaxy.DatasetGenerationTool
• 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.api.galaxy.build_dataset_yaml
• immuneML.api.galaxy.build_yaml_from_arguments
• immuneML.app.ImmuneMLApp
• immuneML.caching.CacheHandler
• immuneML.caching.CacheObjectType
• immuneML.caching.CacheType
• immuneML.data_model.DatasetItem
• immuneML.data_model.cell.Cell
• immuneML.data_model.cell.CellList
• 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.encoded_data.EncodedData
• 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.ReceptorBuilder
• immuneML.data_model.receptor.RegionType
• immuneML.data_model.receptor.TCABReceptor
• immuneML.data_model.receptor.TCGDReceptor
• 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.repertoire.Repertoire
• immuneML.dev_util.util
• immuneML.dsl.DefaultParamsLoader
• immuneML.dsl.ImmuneMLParser
• immuneML.dsl.InstructionParser
• immuneML.dsl.ObjectParser
• immuneML.dsl.OutputParser
• immuneML.dsl.Parser
• 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.import_parsers.ImportParser
• 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.semantic_model.MLResult
• immuneML.dsl.semantic_model.SemanticModel
• immuneML.dsl.symbol_table.SymbolTable
• immuneML.dsl.symbol_table.SymbolTableEntry
• immuneML.dsl.symbol_table.SymbolType
• immuneML.encodings.DatasetEncoder
• immuneML.encodings.EncoderParams
• 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.AtchleyKmerEncoder
• immuneML.encodings.atchley_kmer_encoding.RelativeAbundanceType
• immuneML.encodings.atchley_kmer_encoding.Util
• immuneML.encodings.deeprc.DeepRCEncoder
• immuneML.encodings.distance_encoding.CompAIRRDistanceEncoder
• immuneML.encodings.distance_encoding.DistanceEncoder
• immuneML.encodings.distance_encoding.DistanceMetricType
• immuneML.encodings.distance_encoding.TCRdistEncoder
• immuneML.encodings.evenness_profile.EvennessProfileEncoder
• immuneML.encodings.evenness_profile.EvennessProfileRepertoireEncoder
• 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.GappedKmerSequenceEncoder
• immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder
• immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder
• immuneML.encodings.kmer_frequency.sequence_encoding.IdentitySequenceEncoder
• immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder
• immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy
• immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType
• immuneML.encodings.onehot.OneHotEncoder
• immuneML.encodings.onehot.OneHotReceptorEncoder
• immuneML.encodings.onehot.OneHotRepertoireEncoder
• immuneML.encodings.onehot.OneHotSequenceEncoder
• immuneML.encodings.preprocessing.FeatureScaler
• 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.W2VRepertoireEncoder
• immuneML.encodings.word2vec.W2VSequenceEncoder
• immuneML.encodings.word2vec.Word2VecEncoder
• immuneML.encodings.word2vec.model_creator.KmerPairModelCreator
• immuneML.encodings.word2vec.model_creator.ModelCreatorStrategy
• immuneML.encodings.word2vec.model_creator.ModelType
• immuneML.encodings.word2vec.model_creator.SequenceModelCreator
• immuneML.environment.Constants
• immuneML.environment.EnvironmentSettings
• immuneML.environment.Label
• immuneML.environment.LabelConfiguration
• immuneML.environment.LabelType
• immuneML.environment.SequenceType
• immuneML.hyperparameter_optimization.HPSetting
• immuneML.hyperparameter_optimization.HPSettingResult
• 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.HPAssessment
• immuneML.hyperparameter_optimization.core.HPSelection
• immuneML.hyperparameter_optimization.core.HPUtil
• 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.GridSearch
• immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy
• 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.RandomForestClassifier
• immuneML.ml_methods.ReceptorCNN
• immuneML.ml_methods.SVC
• immuneML.ml_methods.SVM
• immuneML.ml_methods.SklearnMethod
• immuneML.ml_methods.TCRdistClassifier
• immuneML.ml_methods.pytorch_implementations.PyTorchLogisticRegression
• immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN
• immuneML.ml_methods.util.Util
• immuneML.ml_metrics.Metric
• immuneML.ml_metrics.MetricUtil
• immuneML.ml_metrics.ml_metrics
• immuneML.pairwise_repertoire_comparison.ComparisonData
• immuneML.pairwise_repertoire_comparison.ComparisonDataBatch
• immuneML.pairwise_repertoire_comparison.PairwiseRepertoireComparison
• immuneML.preprocessing.Preprocessor
• immuneML.preprocessing.ReferenceSequenceAnnotator
• immuneML.preprocessing.SubjectRepertoireCollector
• 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.presentation.InstructionPresentation
• immuneML.presentation.PresentationFactory
• immuneML.presentation.PresentationFormat
• immuneML.presentation.TemplateParser
• 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.reports.PlotlyUtil
• immuneML.reports.Report
• immuneML.reports.ReportOutput
• immuneML.reports.ReportResult
• immuneML.reports.ReportUtil
• 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.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.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.DiseaseAssociatedSequenceOverlap
• immuneML.reports.multi_dataset_reports.MultiDatasetReport
• immuneML.reports.multi_dataset_reports.PerformanceOverview
• 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.ROCCurveSummary
• immuneML.reports.train_ml_model_reports.ReferenceSequenceOverlap
• immuneML.reports.train_ml_model_reports.TrainMLModelReport
• immuneML.simulation.Implanting
• immuneML.simulation.Simulation
• immuneML.simulation.SimulationState
• immuneML.simulation.dataset_generation.RandomDatasetGenerator
• immuneML.simulation.implants.ImplantAnnotation
• immuneML.simulation.implants.Motif
• immuneML.simulation.implants.MotifInstance
• immuneML.simulation.implants.Signal
• immuneML.simulation.motif_instantiation_strategy.GappedKmerInstantiation
• immuneML.simulation.motif_instantiation_strategy.MotifInstantiationStrategy
• immuneML.simulation.sequence_implanting.GappedMotifImplanting
• immuneML.simulation.sequence_implanting.SequenceImplantingStrategy
• 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.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.instructions.Instruction
• immuneML.workflows.instructions.MLProcess
• immuneML.workflows.instructions.SimulationInstruction
• immuneML.workflows.instructions.TrainMLModelInstruction
• immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction
• immuneML.workflows.instructions.dataset_generation.DatasetExportState
• immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction
• immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState
• immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit
• immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction
• immuneML.workflows.instructions.ml_model_application.MLApplicationState
• immuneML.workflows.instructions.quickstart
• immuneML.workflows.instructions.subsampling.SubsamplingInstruction
• immuneML.workflows.instructions.subsampling.SubsamplingState
• 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
• 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