All modules for which code is available
- mhcflurry.affinity.calibration_sizing
- mhcflurry.affinity.model_selection
- mhcflurry.affinity.persistence
- mhcflurry.allele_encoding
- mhcflurry.amino_acid
- mhcflurry.class1_affinity_predictor
- mhcflurry.class1_affinity_training_data
- mhcflurry.class1_encoding
- mhcflurry.class1_neural_network
- mhcflurry.class1_presentation_predictor
- mhcflurry.class1_processing_neural_network
- mhcflurry.class1_processing_predictor
- mhcflurry.class1_training
- mhcflurry.cli.affinity_candidate_figures
- mhcflurry.cli.calibrate_percentile_ranks_command
- mhcflurry.cli.compare_models
- mhcflurry.cli.downloads_command
- mhcflurry.cli.eval_command
- mhcflurry.cli.experiment_snapshot
- mhcflurry.cli.figure_style
- mhcflurry.cli.generate_training_hyperparameters
- mhcflurry.cli.help
- mhcflurry.cli.main
- mhcflurry.cli.materialize_affinity_checkpoint
- mhcflurry.cli.merge_external_predictions
- mhcflurry.cli.paper_figures
- mhcflurry.cli.plot_loss_curves
- mhcflurry.cli.plot_model_comparison
- mhcflurry.cli.predict_command
- mhcflurry.cli.predict_scan_command
- mhcflurry.cli.processing_affinity_control
- mhcflurry.cli.reassign_mass_spec_training_data
- mhcflurry.cli.select_allele_specific_models_command
- mhcflurry.cli.select_pan_allele_models_command
- mhcflurry.cli.select_processing_models_command
- mhcflurry.cli.train_allele_specific_models_command
- mhcflurry.cli.train_command
- mhcflurry.cli.train_pan_allele_models_command
- mhcflurry.cli.train_presentation_models_command
- mhcflurry.cli.train_processing_models_command
- mhcflurry.cluster_parallelism
- mhcflurry.common
- mhcflurry.compact_percent_rank_transform
- mhcflurry.custom_loss
- mhcflurry.data_dependent_weights_initialization
- mhcflurry.device_footprint
- mhcflurry.downloads
- mhcflurry.encodable_sequences
- mhcflurry.ensemble_centrality
- mhcflurry.experiment_archive
- mhcflurry.fasta
- mhcflurry.flanking_encoding
- mhcflurry.histogram_percent_rank_transform
- mhcflurry.hyperparameters
- mhcflurry.keras_optimizers
- mhcflurry.memory_budget
- mhcflurry.model_provenance
- mhcflurry.motif_summary
- mhcflurry.numeric_proteome
- mhcflurry.numeric_sequences
- mhcflurry.parallelism.cli_args
- mhcflurry.parallelism.planning
- mhcflurry.parallelism.torch_compile
- mhcflurry.parallelism.worker_pool
- mhcflurry.parallelism.worker_runtime
- mhcflurry.peptide_reference
- mhcflurry.percentile_calibration
- mhcflurry.processing_evaluation
- mhcflurry.processing_initialization
- mhcflurry.processing_matching
- mhcflurry.processing_preparation
- mhcflurry.processing_ranking
- mhcflurry.proteome_decoys
- mhcflurry.pseudosequences
- mhcflurry.pytorch_layers
- mhcflurry.pytorch_losses
- mhcflurry.pytorch_sizing
- mhcflurry.pytorch_training
- mhcflurry.random_negative_peptides
- mhcflurry.regression_target
- mhcflurry.release_holdout
- mhcflurry.sample_disjointness
- mhcflurry.scoring
- mhcflurry.scoring_pipeline
- mhcflurry.testing_utils
- mhcflurry.training_benchmark
- mhcflurry.training_folds
- mhcflurry.training_provenance
- mhcflurry.workload_planning