immuneML.workflows.instructions package

Subpackages

• immuneML.workflows.instructions.apply_gen_model package
  • Submodules
  • immuneML.workflows.instructions.apply_gen_model.ApplyGenModelInstruction module
  • Module contents
• immuneML.workflows.instructions.clustering package
  • Submodules
  • immuneML.workflows.instructions.clustering.ClusteringInstruction module
  • immuneML.workflows.instructions.clustering.ClusteringReportHandler module
    • ClusteringReportHandler
      • ClusteringReportHandler.run_clustering_reports()
      • ClusteringReportHandler.run_item_reports()
  • immuneML.workflows.instructions.clustering.ClusteringRunner module
  • immuneML.workflows.instructions.clustering.ClusteringState module
    • ClusteringConfig
      • ClusteringConfig.clustering_settings
      • ClusteringConfig.dataset
      • ClusteringConfig.label_config
      • ClusteringConfig.metrics
      • ClusteringConfig.name
      • ClusteringConfig.region_type
      • ClusteringConfig.sequence_type
      • ClusteringConfig.split_config
      • ClusteringConfig.validation_type
    • ClusteringItemResult
      • ClusteringItemResult.item
      • ClusteringItemResult.report_results
    • ClusteringResultPerRun
      • ClusteringResultPerRun.get_cl_item()
      • ClusteringResultPerRun.items
      • ClusteringResultPerRun.run_id
      • ClusteringResultPerRun.run_type
    • ClusteringResults
      • ClusteringResults.discovery
      • ClusteringResults.method_based_validation
      • ClusteringResults.result_based_validation
    • ClusteringState
      • ClusteringState.add_cl_result_per_run()
      • ClusteringState.clustering_items
      • ClusteringState.clustering_report_results
      • ClusteringState.config
      • ClusteringState.discovery_datasets
      • ClusteringState.name
      • ClusteringState.predictions_paths
      • ClusteringState.result_path
      • ClusteringState.validation_datasets
  • immuneML.workflows.instructions.clustering.ValidationHandler module
  • immuneML.workflows.instructions.clustering.clustering_run_model module
    • ClusteringItem
      • ClusteringItem.cl_setting
      • ClusteringItem.dataset
      • ClusteringItem.encoder
      • ClusteringItem.external_performance
      • ClusteringItem.internal_performance
      • ClusteringItem.method
      • ClusteringItem.predictions
    • ClusteringSetting
      • ClusteringSetting.clustering_method
      • ClusteringSetting.clustering_method_name
      • ClusteringSetting.clustering_params
      • ClusteringSetting.dim_red_name
      • ClusteringSetting.dim_red_params
      • ClusteringSetting.dim_reduction_method
      • ClusteringSetting.encoder
      • ClusteringSetting.encoder_name
      • ClusteringSetting.encoder_params
      • ClusteringSetting.get_key()
      • ClusteringSetting.path
    • DataFrameWrapper
      • DataFrameWrapper.get_df()
  • Module contents
• immuneML.workflows.instructions.dataset_generation package
  • Submodules
  • immuneML.workflows.instructions.dataset_generation.DatasetExportInstruction module
    • DatasetExportInstruction
      • DatasetExportInstruction.get_documentation()
      • DatasetExportInstruction.run()
  • immuneML.workflows.instructions.dataset_generation.DatasetExportState module
    • DatasetExportState
      • DatasetExportState.datasets
      • DatasetExportState.formats
      • DatasetExportState.name
      • DatasetExportState.paths
      • DatasetExportState.preprocessing_sequence
      • DatasetExportState.result_path
  • Module contents
• immuneML.workflows.instructions.exploratory_analysis package
  • Submodules
  • immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction module
    • ExploratoryAnalysisInstruction
      • ExploratoryAnalysisInstruction.encode()
      • ExploratoryAnalysisInstruction.preprocess_dataset()
      • ExploratoryAnalysisInstruction.run()
      • ExploratoryAnalysisInstruction.run_report()
      • ExploratoryAnalysisInstruction.run_unit()
      • ExploratoryAnalysisInstruction.weight_examples()
  • immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState module
    • ExploratoryAnalysisState
      • ExploratoryAnalysisState.exploratory_analysis_units
      • ExploratoryAnalysisState.name
      • ExploratoryAnalysisState.result_path
  • immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit module
    • ExploratoryAnalysisUnit
      • ExploratoryAnalysisUnit.dataset
      • ExploratoryAnalysisUnit.dim_reduction
      • ExploratoryAnalysisUnit.encoder
      • ExploratoryAnalysisUnit.example_weighting
      • ExploratoryAnalysisUnit.label_config
      • ExploratoryAnalysisUnit.number_of_processes
      • ExploratoryAnalysisUnit.preprocessing_sequence
      • ExploratoryAnalysisUnit.report_results
      • ExploratoryAnalysisUnit.reports
  • Module contents
• immuneML.workflows.instructions.ligo_sim_feasibility package
  • Submodules
  • immuneML.workflows.instructions.ligo_sim_feasibility.FeasibilitySummaryInstruction module
    • FeasibilitySumReports
      • FeasibilitySumReports.p_gen_histogram
      • FeasibilitySumReports.seq_len_dist
      • FeasibilitySumReports.signal_cond_probs
      • FeasibilitySumReports.signal_cooccurrences
      • FeasibilitySumReports.signal_frequencies
      • FeasibilitySumReports.signal_joint_probs
      • FeasibilitySumReports.warnings
    • FeasibilitySummaryInstruction
      • FeasibilitySummaryInstruction.MAX_SIG_FREQ
      • FeasibilitySummaryInstruction.MIN_SIG_FREQ
      • FeasibilitySummaryInstruction.run()
    • FeasibilitySummaryState
      • FeasibilitySummaryState.name
      • FeasibilitySummaryState.reports
      • FeasibilitySummaryState.result_path
      • FeasibilitySummaryState.sequence_count
      • FeasibilitySummaryState.signals
      • FeasibilitySummaryState.simulation
  • immuneML.workflows.instructions.ligo_sim_feasibility.feasibility_reports module
    • report_p_gen_histogram()
    • report_seq_len_dist()
    • report_signal_cond_probs()
    • report_signal_cooccurrences()
    • report_signal_frequencies()
    • report_signal_joint_probs()
  • Module contents
• immuneML.workflows.instructions.ligo_simulation package
  • Submodules
  • immuneML.workflows.instructions.ligo_simulation.LigoSimInstruction module
  • immuneML.workflows.instructions.ligo_simulation.runtime_reports module
    • make_p_gen_histogram_plot()
  • Module contents
• immuneML.workflows.instructions.ml_model_application package
  • Submodules
  • immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction module
  • immuneML.workflows.instructions.ml_model_application.MLApplicationState module
  • Module contents
• immuneML.workflows.instructions.subsampling package
  • Submodules
  • immuneML.workflows.instructions.subsampling.SubsamplingInstruction module
    • SubsamplingInstruction
      • SubsamplingInstruction.export_dataset()
      • SubsamplingInstruction.get_documentation()
      • SubsamplingInstruction.make_repertoire_dataset_subset()
      • SubsamplingInstruction.run()
  • immuneML.workflows.instructions.subsampling.SubsamplingState module
    • SubsamplingState
      • SubsamplingState.dataset
      • SubsamplingState.name
      • SubsamplingState.result_path
      • SubsamplingState.subsampled_dataset_paths
      • SubsamplingState.subsampled_dataset_sizes
      • SubsamplingState.subsampled_datasets
      • SubsamplingState.subsampled_repertoire_size
  • Module contents
• immuneML.workflows.instructions.train_gen_model package
  • Submodules
  • immuneML.workflows.instructions.train_gen_model.TrainGenModelInstruction module
  • Module contents

Submodules

immuneML.workflows.instructions.GenModelInstruction module

immuneML.workflows.instructions.Instruction module

class immuneML.workflows.instructions.Instruction.Instruction

Bases: object

abstract run(result_path: Path)

immuneML.workflows.instructions.MLProcess module

immuneML.workflows.instructions.TrainMLModelInstruction module

immuneML.workflows.instructions.quickstart module

Module contents