Index

A

alp_B() (in module damuta.utils) alr() (in module damuta.utils) alr_inv() (in module damuta.utils) annotate_tissue_types() (DataSet method)

annotation (DataSet attribute) approx (HierarchicalTandemLda attribute) (Lda attribute) (TandemLda attribute)

C

Callback (class in damuta.callbacks)

COSMIC_artifact (in module damuta.constants) counts (DataSet attribute)

D

damuta module damuta.base module damuta.callbacks module damuta.constants module damuta.models module

damuta.plotting module damuta.sim module damuta.utils module DataSet (class in damuta.base) dataset (Lda attribute) dirichlet() (in module damuta.utils)

E

encode_counts() (in module damuta.sim)

F

fit() (Lda method)

flatten_eta() (in module damuta.utils) from_damage_misrepair() (SignatureSet class method)

G

get_activities() (Lda method) get_estimated_activities() (TandemLda method) get_estimated_activities_DataFrame() (Lda method) (TandemLda method) get_estimated_connections_DataFrame() (TandemLda method) get_estimated_signatures() (Lda method) (TandemLda method)

get_estimated_SignatureSet() (Lda method) (TandemLda method) get_estimated_W() (HierarchicalTandemLda method) (TandemLda method) get_signatures() (Lda method) get_tau() (in module damuta.utils)

H

HierarchicalTandemLda (class in damuta.models)

I

ids (DataSet property)

idx96 (in module damuta.constants) index (SignatureSet property)

K

kmeans_alr() (in module damuta.utils)

L

lap_B() (in module damuta.utils) Lda (class in damuta.models) load_checkpoint() (in module damuta.utils)

load_dataset() (in module damuta.utils) load_datasets() (in module damuta.utils) LogELBO (class in damuta.callbacks)

M

marginalize_for_eta() (in module damuta.utils) marginalize_for_phi() (in module damuta.utils) model (HierarchicalTandemLda attribute) (Lda attribute) (TandemLda attribute) model_kwargs (HierarchicalTandemLda attribute) (Lda attribute) (TandemLda attribute) module damuta damuta.base damuta.callbacks damuta.constants damuta.models damuta.plotting damuta.sim damuta.utils

mult_ll() (in module damuta.utils) mut16 (in module damuta.constants) mut32 (in module damuta.constants) mut6 (in module damuta.constants) mut96 (in module damuta.constants)

N

n_damage_sigs (SignatureSet property) n_misrepair_sigs (SignatureSet property)

n_samples (DataSet property) n_sigs (Lda attribute) (SignatureSet property)

P

plot_cosmic_signatures() (in module damuta.plotting) plot_damage_signatures() (in module damuta.plotting) plot_eta_posterior() (in module damuta.plotting)

plot_misrepair_signatures() (in module damuta.plotting) plot_phi_posterior() (in module damuta.plotting) plot_signatures() (in module damuta.plotting)

R

run_id (HierarchicalTandemLda attribute) (Lda attribute) (TandemLda attribute)

S

sample_posterior() (Lda method) save_checkpoint() (in module damuta.utils) signatures (SignatureSet attribute)

SignatureSet (class in damuta.base) sim_from_sigs() (in module damuta.sim) sim_parametric() (in module damuta.sim) summarize_separation() (SignatureSet method)

T

TandemLda (class in damuta.models)