Contents:
selectInfoGenes()
SpaMultiDecon_two_modals
SpaMultiDecon_two_modals.weight_loss
SpaMultiDecon_two_modals.hidden_dim
SpaMultiDecon_two_modals.learning_rate
SpaMultiDecon_two_modals.device
SpaMultiDecon_two_modals.epochs
SpaMultiDecon_two_modals.seed
SpaMultiDecon_two_modals.weight_spatial
SpaMultiDecon_two_modals.weight_consistency
SpaMultiDecon_two_modals.pca_n_components_rna
SpaMultiDecon_two_modals.modal2_target_dim
SpaMultiDecon_two_modals.lsi_random_state
SpaMultiDecon_two_modals.set_nn_para()
SpaMultiDecon_two_modals.preprocess()
SpaMultiDecon_two_modals.run_feature_engineering_and_mapping()
SpaMultiDecon_two_modals.create_spatialgraph()
SpaMultiDecon_two_modals.get_laplacian()
SpaMultiDecon_two_modals.create_featuregraph()
SpaMultiDecon_two_modals.train()
set_base_config()
set_analysis_params()
load_and_show_data()
init_model_and_preprocess()
feature_engineering_and_graph_build()
train_model()
clean_anndata_for_save()
save_results()
main()
filter_out_low_quality_data()
process_single_cell()
process_single_cell_path()
sanitize_filename()
normalize_expression_matrix()
normalize_single_cell()
process_spatial_data()
process_spatial_data_path()
get_spatial_hvgs_only()
select_hvgs()
calculate_celltype_averages()
calculate_celltype_averages2()
clr_normalization()
process_spatial_adt_data()
process_spatial_adt_data_path()
process_peak_data()
process_peak_data_path()
set_random_seed()
normalize_coords()
standardize_embedding()
lognorm_transform()
filter_valid_genes()
load_align_data()
project_coords()
RNAFCModel
rna_run()
second_modality_preprocess_single()
second_modality_preprocess_batch()
DenseGCNConv
SecondModalityGCNModel
build_spatial_adj()
second_modality_run()
omics_reconstruct()
get_spatial_xy()
save_spatial_continuous()
save_spatial_categorical()
get_cell_type_proportions()
plot_cell_type_proportion_panel()
plot_all_cell_type_proportions()
plot_individual_cell_type_heatmaps()
plot_embedding_spatial_clustering()
plot_reconstruction_heatmaps()
get_mousebrain_h3k27ac_base_config()
get_mousebrain_h3k27ac_params()
The tutorials demonstrate how to run SMODER, inspect its outputs, and generate downstream visualizations.
See the Results page for representative output figures from the simulated human melanoma, Mousebrain H3K27ac, and HBC datasets.