fennomix_mhc

• fennomix_mhc package
  • Submodules
    • 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()
  • Module contents