fennomix_mhc package¶
Submodules¶
- fennomix_mhc.mhc_binding_model module
- fennomix_mhc.mhc_binding_retriever module
MHCBindingRetrieverMHCBindingRetriever.hla_encoderMHCBindingRetriever.pept_encoderMHCBindingRetriever.deviceMHCBindingRetriever.datasetMHCBindingRetriever.hla_embedsMHCBindingRetriever.n_decoy_samplesMHCBindingRetriever.outlier_thresholdMHCBindingRetriever.use_fmm_fdrMHCBindingRetriever.decoy_rnd_seedMHCBindingRetriever.d_modelMHCBindingRetriever.verboseMHCBindingRetriever.__init__()MHCBindingRetriever.get_binding_distances()MHCBindingRetriever.get_binding_metrics_for_embeds()MHCBindingRetriever.get_binding_metrics_for_peptides()MHCBindingRetriever.get_binding_metrics_for_self_proteins()MHCBindingRetriever.get_embedding_distances()
get_binding_fdr_for_best_allele()get_binding_fdrs()get_binding_ranks()get_fdrs()get_q_values()
- fennomix_mhc.mhc_utils module
- fennomix_mhc.pipeline_api module
PretrainedModelsPretrainedModels.devicePretrainedModels._use_pseudoPretrainedModels.hla_encoderPretrainedModels.pept_encoderPretrainedModels.esm2_modelPretrainedModels.esm2_alphabetPretrainedModels.batch_converterPretrainedModels.background_protein_dfPretrainedModels.hla_dfPretrainedModels.hla_embeddingsPretrainedModels.__init__()PretrainedModels.deconvolute_peptides()PretrainedModels.embed_peptides_from_fasta()PretrainedModels.embed_peptides_tsv()PretrainedModels.embed_proteins()PretrainedModels.predict_epitopes_for_mhc()PretrainedModels.predict_mhc_binders_for_epitopes()
deconvolute_and_predict_peptides()deconvolute_peptides()embed_peptides_from_file()embed_proteins()load_peptide_embedding_pkl()predict_epitopes_for_mhc()predict_mhc_binders_for_epitopes()
- fennomix_mhc.plotting_utils module
- fennomix_mhc.tda_fmm module