Index

_

_captum_deep_lift_shap() (in module tangermeme.deep_lift_shap)

_cast_as_tensor() (in module tangermeme.utils) _validate_input() (in module tangermeme.utils)

A

ablate() (in module tangermeme.ablate) ablate_annotations() (in module tangermeme.ablate)

annotate_seqlets() (in module tangermeme.annotate) apply_product() (in module tangermeme.product)

B

beam_substitution() (in module tangermeme.design.beam_substitution)

C

characters() (in module tangermeme.utils)

chunk() (in module tangermeme.utils) count_annotations() (in module tangermeme.annotate)

D

deep_lift_shap() (in module tangermeme.deep_lift_shap) delete() (in module tangermeme.ersatz)

deletion_effect() (in module tangermeme.variant_effect) dinucleotide_shuffle() (in module tangermeme.ersatz)

E

example_to_fasta_coords() (in module tangermeme.utils) extract_loci() (in module tangermeme.io)

extract_matching_loci() (in module tangermeme.match) extract_signal() (in module tangermeme.utils)

G

gapped_kmers() (in module tangermeme.kmers)

greedy_marginalize() (in module tangermeme.design.greedy_marginalize) greedy_substitution() (in module tangermeme.design.greedy_substitution)

H

hypothetical_attributions() (in module tangermeme.deep_lift_shap)

I

insert() (in module tangermeme.ersatz)

insertion_effect() (in module tangermeme.variant_effect) interactive_logo() (in module tangermeme.plot)

K

kmers() (in module tangermeme.kmers)

M

marginalize() (in module tangermeme.marginalize) marginalize_annotations() (in module tangermeme.marginalize) module tangermeme.ablate tangermeme.annotate tangermeme.deep_lift_shap tangermeme.design.beam_substitution tangermeme.design.greedy_marginalize tangermeme.design.greedy_substitution tangermeme.design.screen tangermeme.ersatz tangermeme.io tangermeme.kmers tangermeme.marginalize tangermeme.match tangermeme.pisa tangermeme.plot tangermeme.predict tangermeme.product tangermeme.saturation_mutagenesis tangermeme.seqlet tangermeme.space tangermeme.utils tangermeme.variant_effect

multisubstitute() (in module tangermeme.ersatz)

O

one_hot_encode() (in module tangermeme.utils)

P

pairwise_annotations() (in module tangermeme.annotate) pairwise_annotations_spacing() (in module tangermeme.annotate) pisa() (in module tangermeme.pisa)

plot_logo() (in module tangermeme.plot) predict() (in module tangermeme.predict) pwm_consensus() (in module tangermeme.utils)

R

random_one_hot() (in module tangermeme.utils) randomize() (in module tangermeme.ersatz) read_meme() (in module tangermeme.io)

read_vcf() (in module tangermeme.io) recursive_seqlets() (in module tangermeme.seqlet) reverse_complement() (in module tangermeme.utils)

S

saturation_mutagenesis() (in module tangermeme.saturation_mutagenesis) screen() (in module tangermeme.design.screen) shuffle() (in module tangermeme.ersatz)

space() (in module tangermeme.space) substitute() (in module tangermeme.ersatz) substitution_effect() (in module tangermeme.variant_effect)

T

tangermeme.ablate module tangermeme.annotate module tangermeme.deep_lift_shap module tangermeme.design.beam_substitution module tangermeme.design.greedy_marginalize module tangermeme.design.greedy_substitution module tangermeme.design.screen module tangermeme.ersatz module tangermeme.io module tangermeme.kmers module tangermeme.marginalize module

tangermeme.match module tangermeme.pisa module tangermeme.plot module tangermeme.predict module tangermeme.product module tangermeme.saturation_mutagenesis module tangermeme.seqlet module tangermeme.space module tangermeme.utils module tangermeme.variant_effect module tfmodisco_seqlets() (in module tangermeme.seqlet)

U

unchunk() (in module tangermeme.utils)