Index

A

add_deconvolution() (in module stlearn.add) add_loupe_clusters() (in module stlearn.add) add_mask() (in module stlearn.add)

adj_pvals() (in module stlearn.tl.cci) adjust() (in module stlearn.spatial.morphology) annotation() (in module stlearn.add) apply_mask() (in module stlearn.add)

C

cci_check() (in module stlearn.pl) cci_map() (in module stlearn.pl) ccinet_plot() (in module stlearn.pl) cluster_plot() (in module stlearn.pl)

cluster_plot_interactive() (in module stlearn.pl) compare_transitions() (in module stlearn.spatial.trajectory) convert_scanpy() (in module stlearn) create_stlearn() (in module stlearn)

D

DE_transition_plot() (in module stlearn.pl.trajectory) deconvolution_plot() (in module stlearn.pl)

detect_transition_markers_branches() (in module stlearn.spatial.trajectory) detect_transition_markers_clades() (in module stlearn.spatial.trajectory)

E

extract_feature() (in module stlearn.pp)

F

filter_genes() (in module stlearn.pp)

G

gene_plot() (in module stlearn.pl)

gene_plot_interactive() (in module stlearn.pl) grid() (in module stlearn.tl.cci)

I

image() (in module stlearn.add)

K

kmeans() (in module stlearn.tl.clustering)

L

labels() (in module stlearn.add) load_lrs() (in module stlearn.tl.cci) local_plot() (in module stlearn.pl.trajectory) localization() (in module stlearn.spatial.clustering) log1p() (in module stlearn.pp) louvain() (in module stlearn.tl.clustering) lr() (in module stlearn.add) lr_cci_map() (in module stlearn.pl)

lr_chord_plot() (in module stlearn.pl) lr_diagnostics() (in module stlearn.pl) lr_go() (in module stlearn.pl) lr_n_spots() (in module stlearn.pl) lr_plot() (in module stlearn.pl) lr_plot_interactive() (in module stlearn.pl) lr_result_plot() (in module stlearn.pl) lr_summary() (in module stlearn.pl)

M

module stlearn stlearn.em stlearn.pp stlearn.spatial.clustering stlearn.spatial.morphology stlearn.spatial.SME stlearn.spatial.trajectory

N

neighbors() (in module stlearn.pp)

non_spatial_plot() (in module stlearn.pl) normalize_total() (in module stlearn.pp)

P

parsing() (in module stlearn.add) plot_mask() (in module stlearn.pl) positions() (in module stlearn.add) pseudo_spot() (in module stlearn.spatial.SME)

pseudotime() (in module stlearn.spatial.trajectory) pseudotime_plot() (in module stlearn.pl.trajectory) pseudotimespace_global() (in module stlearn.spatial.trajectory) pseudotimespace_local() (in module stlearn.spatial.trajectory)

Q

QC_plot() (in module stlearn.pl)

R

Read10X() (in module stlearn) ReadMERFISH() (in module stlearn) ReadOldST() (in module stlearn) ReadSeqFish() (in module stlearn) ReadSlideSeq() (in module stlearn) run() (in module stlearn.tl.cci)

run_cci() (in module stlearn.tl.cci) run_diffmap() (in module stlearn.em) run_fa() (in module stlearn.em) run_ica() (in module stlearn.em) run_lr_go() (in module stlearn.tl.cci) run_pca() (in module stlearn.em) run_umap() (in module stlearn.em)

S

scale() (in module stlearn.pp) set_root() (in module stlearn.spatial.trajectory) SME_impute0() (in module stlearn.spatial.SME) SME_normalize() (in module stlearn.spatial.SME) spatialcci_plot_interactive() (in module stlearn.pl) stlearn module stlearn.em module stlearn.pp module

stlearn.spatial.clustering module stlearn.spatial.morphology module stlearn.spatial.SME module stlearn.spatial.trajectory module subcluster_plot() (in module stlearn.pl)

T

tiling() (in module stlearn.pp)

transition_markers_plot() (in module stlearn.pl.trajectory) tree_plot() (in module stlearn.pl.trajectory)

V

visium_sge() (in module stlearn.datasets)

X

xenium_sge() (in module stlearn.datasets)