Index

B

batch() (in module polygraph.models)

bleu_similarity() (in module polygraph.sequence) boxplot() (in module polygraph.visualize)

C

cell_type_specificity() (in module polygraph.models) CharDataset (class in polygraph.likelihood)

check_equal_lens() (in module polygraph.utils) compute_likelihood() (in module polygraph.likelihood)

D

densityplot() (in module polygraph.visualize)

download_gtex_tpm() (in module polygraph.input) download_jaspar() (in module polygraph.input)

E

encode() (polygraph.likelihood.CharDataset method)

enformer_embed() (in module polygraph.models) evolve() (in module polygraph.evolve)

F

fastsk() (in module polygraph.sequence)

G

gc() (in module polygraph.sequence) get_embeddings() (in module polygraph.models) get_lens() (in module polygraph.utils) get_motif_pairs() (in module polygraph.motifs)

groupwise_fishers() (in module polygraph.stats) groupwise_mann_whitney() (in module polygraph.stats) groupwise_mean_edit_dist() (in module polygraph.sequence) groupwise_svm() (in module polygraph.classifier)

I

integer_encode() (in module polygraph.utils)

ISM() (in module polygraph.sequence) ism_score() (in module polygraph.models)

K

kmer_frequencies() (in module polygraph.sequence)

kmer_positions() (in module polygraph.sequence) kruskal_dunn() (in module polygraph.stats)

L

load_enformer() (in module polygraph.models) load_gtex_tpm() (in module polygraph.input)

load_hyenadna() (in module polygraph.likelihood) load_nucleotide_transformer() (in module polygraph.models)

M

make_ids() (in module polygraph.utils) min_edit_distance() (in module polygraph.sequence) min_edit_distance_from_reference() (in module polygraph.sequence) module polygraph polygraph.classifier polygraph.evolve polygraph.input polygraph.likelihood polygraph.models polygraph.motifs polygraph.sequence polygraph.stats polygraph.utils polygraph.visualize

motif_frequencies() (in module polygraph.motifs) motif_pair_differential_abundance() (in module polygraph.motifs) motif_pair_differential_distance() (in module polygraph.motifs) motif_pair_differential_orientation() (in module polygraph.motifs)

N

nmf() (in module polygraph.motifs)

nucleotide_transformer_embed() (in module polygraph.models)

O

one_nn_frac_plot() (in module polygraph.visualize)

P

pad_with_Ns() (in module polygraph.utils) pca_plot() (in module polygraph.visualize) plot_factors_nmf() (in module polygraph.visualize) plot_seqs_nmf() (in module polygraph.visualize) polygraph module polygraph.classifier module polygraph.evolve module polygraph.input module polygraph.likelihood module

polygraph.models module polygraph.motifs module polygraph.sequence module polygraph.stats module polygraph.utils module polygraph.visualize module predict() (in module polygraph.models)

R

read_meme_file() (in module polygraph.input) read_seqs() (in module polygraph.input)

reverse_complement() (in module polygraph.utils) robustness() (in module polygraph.models)

S

scan() (in module polygraph.motifs)

score_sites() (in module polygraph.motifs) sequential_embed() (in module polygraph.models)

U

umap_plot() (in module polygraph.visualize)

unique_kmers() (in module polygraph.sequence) upset_plot() (in module polygraph.visualize)