polygraph

• polygraph package
  • Submodules
  • polygraph.classifier module
    • groupwise_svm()
  • polygraph.embedding module
  • polygraph.evolve module
    • evolve()
  • polygraph.input module
    • download_gtex_tpm()
    • download_jaspar()
    • load_gtex_tpm()
    • read_meme_file()
    • read_seqs()
  • polygraph.likelihood module
    • CharDataset
      • CharDataset.encode()
    • compute_likelihood()
    • load_hyenadna()
  • polygraph.models module
    • batch()
    • cell_type_specificity()
    • enformer_embed()
    • get_embeddings()
    • ism_score()
    • load_enformer()
    • load_nucleotide_transformer()
    • nucleotide_transformer_embed()
    • predict()
    • robustness()
    • sequential_embed()
  • polygraph.motifs module
    • get_motif_pairs()
    • motif_frequencies()
    • motif_pair_differential_abundance()
    • motif_pair_differential_distance()
    • motif_pair_differential_orientation()
    • nmf()
    • scan()
    • score_sites()
  • polygraph.sequence module
    • ISM()
    • bleu_similarity()
    • fastsk()
    • gc()
    • groupwise_mean_edit_dist()
    • kmer_frequencies()
    • kmer_positions()
    • min_edit_distance()
    • min_edit_distance_from_reference()
    • unique_kmers()
  • polygraph.stats module
    • groupwise_fishers()
    • groupwise_mann_whitney()
    • kruskal_dunn()
  • polygraph.utils module
    • check_equal_lens()
    • get_lens()
    • integer_encode()
    • make_ids()
    • pad_with_Ns()
    • reverse_complement()
  • polygraph.visualize module
    • boxplot()
    • densityplot()
    • one_nn_frac_plot()
    • pca_plot()
    • plot_factors_nmf()
    • plot_seqs_nmf()
    • umap_plot()
    • upset_plot()
  • Module contents