• fennomix_mhc
  • fennomix_mhc package
• fennomix_mhc package
  • Submodules
  • Module contents
• fennomix_mhc.mhc_binding_model module
  • HlaDataSet
  • ModelHlaEncoder
  • ModelSeqEncoder
  • SiameseCELoss
  • batchify_hla_esm_list()
  • embed_hla_esm_list()
  • embed_peptides()
  • get_ascii_indices()
  • get_cosine_schedule_with_warmup()
  • get_hla_dataloader()
  • pept_hla_collate()
  • test()
  • train()
• fennomix_mhc.mhc_binding_retriever module
  • MHCBindingRetriever
  • get_binding_fdr_for_best_allele()
  • get_binding_fdrs()
  • get_binding_ranks()
  • get_fdrs()
  • get_q_values()
• fennomix_mhc.mhc_utils module
  • NonSpecificDigest
  • load_peptide_df_from_mixmhcpred()
• fennomix_mhc.pipeline_api module
  • PretrainedModels
  • 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
  • adjust_axes()
  • count_motif_bits()
  • fit_hla_umap_reducer()
  • plot_motif()
  • plot_motif_multi_mer()
  • plot_umap_df()
  • select_optimal_a_cover()
  • transform_embeds_to_tSNE_df()
  • transform_embeds_to_umap_df()
  • transform_matrix_to_mds_df()
• fennomix_mhc.tda_fmm module
  • DecoyModel
  • TDA_fmm
  • gamma_pdf()
  • gauss_pdf()
  • select_best_fmm()