Index

A

append_factors() (starfysh.utils.VisiumArguments method) append_sigs() (in module starfysh.utils) ArchetypalAnalysis (class in starfysh.AA)

arg_constraints (starfysh.starfysh.NegBinom attribute) assign_archetypes() (starfysh.AA.ArchetypalAnalysis method) AVAE (class in starfysh.starfysh) AVAE_PoE (class in starfysh.starfysh)

C

compute_archetypes() (starfysh.AA.ArchetypalAnalysis method)

create_corr_network_5() (in module starfysh.post_analysis)

D

display_reconst() (in module starfysh.post_analysis)

E

extract_feature() (in module starfysh.utils)

F

filter_gene_sig() (in module starfysh.utils) find_archetypal_spots() (starfysh.AA.ArchetypalAnalysis method)

find_distant_archetypes() (starfysh.AA.ArchetypalAnalysis method) find_markers() (starfysh.AA.ArchetypalAnalysis method)

G

gene_mean_vs_inferred_prop() (in module starfysh.post_analysis) generative() (starfysh.starfysh.AVAE method) (starfysh.starfysh.AVAE_PoE method) get_adata() (in module starfysh.post_analysis) (starfysh.utils.VisiumArguments method) get_adata_wsig() (in module starfysh.utils) get_alpha_min() (in module starfysh.utils) get_anchor_spots() (in module starfysh.utils) get_anchors() (starfysh.utils.VisiumArguments method) get_cormtx() (in module starfysh.post_analysis) get_corr_map() (in module starfysh.post_analysis)

get_factor_dist() (in module starfysh.post_analysis) get_hub_cormtx() (in module starfysh.post_analysis) get_img_patches() (starfysh.utils.VisiumArguments method) get_LISA() (in module starfysh.post_analysis) get_loss() (starfysh.starfysh.AVAE method) (starfysh.starfysh.AVAE_PoE method) get_Moran() (in module starfysh.post_analysis) get_SCI() (in module starfysh.post_analysis) get_simu_map_info() (in module starfysh.utils) get_umap() (in module starfysh.utils) get_windowed_library() (in module starfysh.utils) get_z_umap() (in module starfysh.post_analysis)

I

inference() (starfysh.starfysh.AVAE method) (starfysh.starfysh.AVAE_PoE method)

init_weights() (in module starfysh.utils)

L

load_adata() (in module starfysh.utils)

load_signatures() (in module starfysh.utils) log_prob() (starfysh.starfysh.NegBinom method)

M

model_ct_exp() (in module starfysh.starfysh) model_eval() (in module starfysh.starfysh) module starfysh starfysh.AA starfysh.dataloader starfysh.plot_utils starfysh.post_analysis starfysh.starfysh starfysh.utils

N

NegBinom (class in starfysh.starfysh)

P

pl_spatial_inf_feature() (in module starfysh.plot_utils) pl_spatial_inf_gene() (in module starfysh.plot_utils) pl_umap_feature() (in module starfysh.plot_utils) plot_anchor_archetype_clusters() (starfysh.AA.ArchetypalAnalysis method) plot_anchor_spots() (in module starfysh.plot_utils) plot_archetypes() (starfysh.AA.ArchetypalAnalysis method) plot_density() (in module starfysh.post_analysis) plot_evs() (in module starfysh.plot_utils)

plot_mapping() (starfysh.AA.ArchetypalAnalysis method) plot_spatial_feature() (in module starfysh.plot_utils) plot_spatial_gene() (in module starfysh.plot_utils) plot_stacked_prop() (in module starfysh.post_analysis) plot_type_all() (in module starfysh.post_analysis) predict_imgVAE() (starfysh.starfysh.AVAE_PoE method) predictor_POE() (starfysh.starfysh.AVAE_PoE method) preprocess() (in module starfysh.utils) preprocess_img() (in module starfysh.utils)

R

refine_anchors() (in module starfysh.utils) reparameterize() (starfysh.starfysh.AVAE method) (starfysh.starfysh.AVAE_PoE method)

replace_factors() (starfysh.utils.VisiumArguments method) run_starfysh() (in module starfysh.utils)

S

sample() (starfysh.starfysh.NegBinom method) starfysh module starfysh.AA module starfysh.dataloader module starfysh.plot_utils module

starfysh.post_analysis module starfysh.starfysh module starfysh.utils module support (starfysh.starfysh.NegBinom attribute)

T

train() (in module starfysh.starfysh) train_poe() (in module starfysh.starfysh)

training (starfysh.starfysh.AVAE attribute) (starfysh.starfysh.AVAE_PoE attribute)

V

valid_model() (in module starfysh.starfysh) VisiumArguments (class in starfysh.utils)

VisiumDataset (class in starfysh.dataloader) VisiumPoEDataSet (class in starfysh.dataloader)