Index

A

adapt_banksy_for_multisample() (in module xb.domain_identification), [1] allcombs() (in module xb.simulating), [1]

allcombs_simulated() (in module xb.simulating), [1] alphashape_fun() (in module xb.calculating), [1]

B

batch_prep_xenium_data_for_baysor() (in module xb.formatting), [1]

C

cell_area() (in module xb.formatting), [1] coexpression_calculation() (in module xb.calculating), [1] combine_med() (in module xb.comparing), [1] compare_domains() (in module xb.domain_identification), [1] components_ (xb.Spage_main.PLS property), [1]

compute_fmi() (in module xb.calculating), [1] (in module xb.simulating), [1] compute_nmi() (in module xb.calculating), [1] compute_principal_vectors() (xb.Spage_main.PVComputation method), [1] compute_vi() (in module xb.calculating), [1] (in module xb.simulating), [1]

D

define_palette() (in module xb.domain_identification), [1] dispersion() (in module xb.calculating), [1] dist_nuc() (in module xb.calculating), [1] distance_calc() (in module xb.calculating), [1]

domainassign() (in module xb.calculating), [1] domains_by_banksy() (in module xb.domain_identification), [1] domains_by_nbd() (in module xb.domain_identification), [1] domains_by_rbd() (in module xb.domain_identification), [1]

E

entropy() (in module xb.calculating), [1] (in module xb.simulating), [1]

F

fit() (xb.Spage_main.PLS method), [1] (xb.Spage_main.PVComputation method), [1] format_background() (in module xb.formatting), [1] format_baysor_output_to_adata() (in module xb.formatting), [1] format_data_neighs() (in module xb.domain_identification), [1] (in module xb.formatting), [1]

format_data_neighs_colapse() (in module xb.domain_identification), [1] (in module xb.formatting), [1] format_to_adata() (in module xb.formatting), [1] format_xenium_adata() (in module xb.formatting), [1] format_xenium_adata_2023() (in module xb.formatting), [1] format_xenium_adata_final() (in module xb.formatting), [1] format_xenium_adata_mid_2023() (in module xb.formatting), [1]

G

gene_imputation() (in module xb.Spage_main), [1] generate_hex_colors() (in module xb.plotting), [1]

generate_random_color_variation() (in module xb.formatting), [1] get_components_() (xb.Spage_main.PLS method), [1]

H

hex_to_rgb() (in module xb.calculating), [1]

K

keep_nuclei() (in module xb.formatting), [1]

keep_nuclei_and_quality() (in module xb.formatting), [1] (in module xb.simulating), [1]

L

leave_one_out_validation() (in module xb.Spage_main), [1]

M

main_preprocessing() (in module xb.preprocessing), [1] (in module xb.simulating), [1] map_of_clusters() (in module xb.plotting), [1] median_calculator() (in module xb.comparing), [1] missegmentation_simulation() (in module xb.simulating), [1] module xb.calculating, [1] xb.comparing, [1] xb.domain_identification, [1] xb.formatting, [1] xb.neighborhood, [1] xb.plotting, [1] xb.preprocessing, [1] xb.simulating, [1] xb.Spage_main, [1]

N

negative_marker_purity_coexpression() (in module xb.calculating), [1]

nhood_squidpy() (in module xb.neighborhood), [1] noise_adder() (in module xb.simulating), [1]

P

plot_cell_counts() (in module xb.plotting), [1] plot_domains() (in module xb.plotting), [1] PLS (class in xb.Spage_main), [1] predict() (xb.Spage_main.PLS method), [1]

prep_xenium_data_for_baysor() (in module xb.formatting), [1] preprocess_adata() (in module xb.preprocessing), [1] process_dim_reduction() (in module xb.Spage_main), [1] PVComputation (class in xb.Spage_main), [1]

S

set_components_() (xb.Spage_main.PLS method), [1] SpaGE() (in module xb.Spage_main), [1]

spatial_plot() (in module xb.domain_identification), [1] subset_of_single_cell() (in module xb.simulating), [1] svf_moranI() (in module xb.calculating), [1]

T

transform() (xb.Spage_main.PLS method), [1] (xb.Spage_main.PVComputation method), [1]

X

xb.calculating module, [1] xb.comparing module, [1] xb.domain_identification module, [1] xb.formatting module, [1] xb.neighborhood module, [1]

xb.plotting module, [1] xb.preprocessing module, [1] xb.simulating module, [1] xb.Spage_main module, [1]