Index

_

__init__() (seam.attributer.Attributer method) (seam.clusterer.Clusterer method) (seam.compiler.Compiler method) (seam.identifier.Identifier method) (seam.meta_explainer.MetaExplainer method)

A

active_clusters_by_tfbs (seam.identifier.Identifier attribute)

arr2pd() (in module seam.utils) Attributer (class in seam.attributer)

B

bpnet_counts() (seam.attributer.Attributer static method)

bpnet_profile() (seam.attributer.Attributer static method)

C

calculate_background_entropy() (in module seam.utils) cluster() (seam.clusterer.Clusterer method) cluster_msm_covariance() (seam.identifier.Identifier method) Clusterer (class in seam.clusterer)

compile() (seam.compiler.Compiler method) Compiler (class in seam.compiler) compute() (seam.attributer.Attributer method) compute_background() (seam.meta_explainer.MetaExplainer method) cov_matrix (seam.identifier.Identifier attribute)

D

DEFAULT_BATCH_SIZES (seam.attributer.Attributer attribute)

E

embed() (seam.clusterer.Clusterer method)

entropy_multiplier (seam.identifier.Identifier attribute)

G

generate_logos() (seam.meta_explainer.MetaExplainer method) generate_msm() (seam.meta_explainer.MetaExplainer method) get_additive_params() (seam.identifier.Identifier method) get_binding_config_assignments() (seam.identifier.Identifier method) get_binding_config_matrix() (seam.identifier.Identifier method)

get_cluster_labels() (seam.clusterer.Clusterer method) get_cluster_maps() (seam.meta_explainer.MetaExplainer method) get_cluster_order() (seam.meta_explainer.MetaExplainer method) get_device() (in module seam.utils) get_epistatic_params() (seam.identifier.Identifier method) get_tfbs_positions() (seam.identifier.Identifier method)

I

Identifier (class in seam.identifier)

intgrad() (seam.attributer.Attributer method) ism() (seam.attributer.Attributer method)

M

MetaExplainer (class in seam.meta_explainer) module seam.attributer seam.clusterer seam.compiler seam.identifier seam.meta_explainer seam.utils

N

normalize() (seam.clusterer.Clusterer method)

O

oh2seq() (in module seam.utils)

P

plot_attribution_variation() (seam.meta_explainer.MetaExplainer method) plot_binding_config_matrix() (seam.identifier.Identifier method) plot_cluster_profiles() (seam.meta_explainer.MetaExplainer method) plot_cluster_stats() (seam.meta_explainer.MetaExplainer method) plot_dendrogram() (seam.clusterer.Clusterer method) plot_embedding() (seam.clusterer.Clusterer method)

plot_epistatic_interactions() (seam.identifier.Identifier method) plot_histogram() (seam.clusterer.Clusterer method) plot_msm() (seam.meta_explainer.MetaExplainer method) plot_msm_covariance_dendrogram() (seam.identifier.Identifier method) plot_msm_covariance_square() (seam.identifier.Identifier method) plot_msm_covariance_triangular() (seam.identifier.Identifier method) plot_pairwise_matrix() (seam.identifier.Identifier method)

R

revels (seam.identifier.Identifier attribute)

S

safe_file_path() (in module seam.utils) saliency() (seam.attributer.Attributer method) seam.attributer module seam.clusterer module seam.compiler module seam.identifier module seam.meta_explainer module

seam.utils module seq2oh() (in module seam.utils) set_entropy_multiplier() (seam.identifier.Identifier method) show_params() (seam.attributer.Attributer method) show_sequences() (seam.meta_explainer.MetaExplainer method) smoothgrad() (seam.attributer.Attributer method) SUPPORTED_CLUSTERERS (seam.clusterer.Clusterer attribute) SUPPORTED_METHODS (seam.attributer.Attributer attribute) (seam.clusterer.Clusterer attribute) suppress_warnings() (in module seam.utils)

T

tfbs_clusters (seam.identifier.Identifier attribute)