All modules for which code is available
- immuneML.IO.dataset_export.AIRRExporter
- immuneML.IO.dataset_export.DataExporter
- 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.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.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.app.ImmuneMLApp
- immuneML.caching.CacheHandler
- immuneML.caching.CacheObjectType
- immuneML.caching.CacheType
- 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.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.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.SVC
- immuneML.ml_methods.classifiers.SVM
- immuneML.ml_methods.classifiers.SklearnMethod
- immuneML.ml_methods.classifiers.TCRdistClassifier
- 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.PyTorchLogisticRegression
- immuneML.ml_methods.pytorch_implementations.PyTorchReceptorCNN
- immuneML.ml_methods.util.Util
- 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.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.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.gen_model_reports.GenModelReport
- immuneML.reports.gen_model_reports.VAESummary
- 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.dataset_generation.RandomDatasetGenerator
- immuneML.simulation.implants.ImplantAnnotation
- immuneML.simulation.implants.Motif
- immuneML.simulation.implants.MotifInstance
- immuneML.simulation.implants.Signal
- immuneML.simulation.simulation_strategy.ImplantingStrategy
- immuneML.simulation.simulation_strategy.RejectionSamplingStrategy
- immuneML.simulation.simulation_strategy.SimulationStrategy
- immuneML.simulation.util.bnp_util
- immuneML.simulation.util.igor_helper
- immuneML.simulation.util.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.instructions.Instruction
- immuneML.workflows.instructions.MLProcess
- 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.ligo_sim_feasibility.FeasibilitySummaryInstruction
- immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports
- immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction
- 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.instructions.train_gen_model.TrainGenModelInstruction
- 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
- 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