Index

_

__init__() (spared.models.ImageEncoder method)

A

add_noisy_layer() (in module spared.layer_operations)

C

combat_transformation() (in module spared.layer_operations) compute_dim_red() (in module spared.spot_features)

compute_moran() (in module spared.gene_features) compute_patches_embeddings() (in module spared.spot_features) compute_patches_predictions() (in module spared.spot_features)

F

filter_by_moran() (in module spared.filtering)

filter_dataset() (in module spared.filtering)

G

get_dataset() (in module spared.datasets) get_deltas() (in module spared.layer_operations) get_exp_frac() (in module spared.gene_features) get_glob_exp_frac() (in module spared.gene_features) get_graph_dataloaders() (in module spared.dataloaders) get_graphs() (in module spared.graph_operations) get_graphs_one_slide() (in module spared.graph_operations)

get_metrics() (in module spared.metrics) get_pearsonr() (in module spared.metrics) get_pretrain_dataloaders() (in module spared.dataloaders) get_r2_score() (in module spared.metrics) get_sin_cos_positional_embeddings() (in module spared.graph_operations) get_slide_from_collection() (in module spared.filtering) get_slides_adata() (in module spared.filtering) get_spatial_neighbors() (in module spared.spot_features)

I

ImageEncoder (class in spared.models)

L

log1p_transformation() (in module spared.layer_operations)

M

median_cleaner() (in module spared.denoising) module spared.dataloaders spared.datasets spared.denoising spared.filtering spared.gene_features spared.graph_operations spared.layer_operations spared.metrics spared.models spared.plotting spared.spot_features

P

plot_all_slides() (in module spared.plotting) plot_clusters() (in module spared.plotting) plot_data_distribution_stats() (in module spared.plotting) plot_exp_frac() (in module spared.plotting) plot_histograms() (in module spared.plotting)

plot_mean_std() (in module spared.plotting) plot_mean_std_partitions() (in module spared.plotting) plot_random_patches() (in module spared.plotting) plot_tests() (in module spared.plotting) process_dataset() (in module spared.layer_operations)

S

spackle_cleaner() (in module spared.denoising) spared.dataloaders module spared.datasets module spared.denoising module spared.filtering module spared.gene_features module

spared.graph_operations module spared.layer_operations module spared.metrics module spared.models module spared.plotting module spared.spot_features module

T

tpm_normalization() (in module spared.layer_operations)

V

visualize_gene_expression() (in module spared.plotting)

visualize_moran_filtering() (in module spared.plotting)