Index

A

adata_to_mtx_conversion() (in module thor.analy)

analyze_gene_expression_gradient() (in module thor.analy) annotate_ROI() (in module thor.pl)

C

clusters() (in module thor.pl)

compute_dge_between_regions() (in module thor.analy) compute_pattern_mean() (thor.analy.SPARKX static method)

D

deg() (in module thor.pl)

F

fineST (class in thor)

fringe() (in module thor.pl)

G

get_bbox() (thor.pp.WholeSlideImage static method) get_pathway_score() (in module thor.analy)

get_reduced_genes() (thor.fineST method) get_tf_activity() (in module thor.analy)

H

hierarchy_clustering() (thor.analy.SPARKX method)

K

kmeans_clustering() (thor.analy.SPARKX method)

L

load() (thor.fineST class method) load_cellpose() (in module thor.pp) load_cellprofiler() (in module thor.pp) load_external_cell_features() (thor.pp.WholeSlideImage method) load_gene_modules() (thor.analy.SPARKX method) load_genes() (thor.fineST method)

load_mask_npz() (in module thor.pp) load_nuclei() (in module thor.pp) load_params() (thor.fineST method) load_result() (thor.analy.SPARKX method) (thor.fineST method) load_vae_model() (thor.fineST method)

M

multi_molecules() (in module thor.pl)

multiple() (in module thor.pl)

N

nuclei_segmentation() (in module thor.pp) (thor.pp.WholeSlideImage method)

P

predict_gene_expression() (thor.fineST method) prepare_and_run_copykat() (in module thor.analy) prepare_input() (thor.fineST method)

prepare_recipe() (thor.fineST method) preprocess_image() (in module thor.pp) process() (thor.pp.WholeSlideImage method) process_transcriptome() (thor.pp.Spatial method)

R

read_polygon_ROI() (in module thor.analy)

run_commot() (in module thor.analy) RUN_SPARKX_R() (thor.analy.SPARKX method)

S

sanity_check() (thor.fineST method) save() (thor.fineST method) set_cell_features_csv_path() (thor.fineST method) set_cell_features_list() (thor.fineST method) set_genes_for_prediction() (thor.fineST method) set_params() (thor.fineST method)

single() (in module thor.pl) single_molecule() (in module thor.pl) SPARKX (class in thor.analy) Spatial (class in thor.pp) split() (thor.pp.WholeSlideImage method) spot_over() (in module thor.pl)

V

vae_training() (thor.fineST method)

visualize_cell_network() (thor.fineST method)

W

WholeSlideImage (class in thor.pp)

write_adata() (thor.fineST method) write_params() (thor.fineST method)