fennomix_mhc package

Submodules

• fennomix_mhc.mhc_binding_model module
  • HlaDataSet
    • HlaDataSet.__init__()
    • HlaDataSet.get_allele_embed()
    • HlaDataSet.get_neg_pept()
  • ModelHlaEncoder
    • ModelHlaEncoder.__init__()
    • ModelHlaEncoder.forward()
  • ModelSeqEncoder
    • ModelSeqEncoder.__init__()
    • ModelSeqEncoder.forward()
  • SiameseCELoss
    • SiameseCELoss.get_loss()
    • SiameseCELoss.margin
  • 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
    • MHCBindingRetriever.hla_encoder
    • MHCBindingRetriever.pept_encoder
    • MHCBindingRetriever.device
    • MHCBindingRetriever.dataset
    • MHCBindingRetriever.hla_embeds
    • MHCBindingRetriever.n_decoy_samples
    • MHCBindingRetriever.outlier_threshold
    • MHCBindingRetriever.use_fmm_fdr
    • MHCBindingRetriever.decoy_rnd_seed
    • MHCBindingRetriever.d_model
    • MHCBindingRetriever.verbose
    • MHCBindingRetriever.__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
  • NonSpecificDigest
    • NonSpecificDigest.__init__()
    • NonSpecificDigest.get_peptide_seqs_from_idxes()
    • NonSpecificDigest.get_random_pept_df()
  • load_peptide_df_from_mixmhcpred()
• fennomix_mhc.pipeline_api module
  • PretrainedModels
    • PretrainedModels.device
    • PretrainedModels._use_pseudo
    • PretrainedModels.hla_encoder
    • PretrainedModels.pept_encoder
    • PretrainedModels.esm2_model
    • PretrainedModels.esm2_alphabet
    • PretrainedModels.batch_converter
    • PretrainedModels.background_protein_df
    • PretrainedModels.hla_df
    • PretrainedModels.hla_embeddings
    • PretrainedModels.__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
  • 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
    • DecoyModel.__init__()
    • DecoyModel.fit()
    • DecoyModel.pdf()
  • TDA_fmm
    • TDA_fmm.n_components
    • TDA_fmm.external_model
    • TDA_fmm.max_iter
    • TDA_fmm.main_pdf
    • TDA_fmm.helper_pdf
    • TDA_fmm.weights
    • TDA_fmm.mu
    • TDA_fmm.sigma
    • TDA_fmm.__init__()
    • TDA_fmm.fit()
    • TDA_fmm.get_pi0()
    • TDA_fmm.loglik_BIC()
    • TDA_fmm.pdf()
    • TDA_fmm.pdf_mix()
    • TDA_fmm.pep()
    • TDA_fmm.plot()
  • gamma_pdf()
  • gauss_pdf()
  • select_best_fmm()

Module contents

https://fennomix-mhc.readthedocs.io/en/latest/