Index

B

build_spatial_adj() (in module smoder.postprocessing.reconstruction)

C

calculate_celltype_averages() (in module smoder.preprocessing.rna) calculate_celltype_averages2() (in module smoder.preprocessing.rna) clean_anndata_for_save() (in module smoder.pipelines.mousebrain_h3k27ac)

clr_normalization() (in module smoder.preprocessing.modality2) create_featuregraph() (smoder.models.deconvolution.SpaMultiDecon_two_modals method) create_spatialgraph() (smoder.models.deconvolution.SpaMultiDecon_two_modals method)

D

DenseGCNConv (class in smoder.postprocessing.reconstruction)

device (smoder.models.deconvolution.SpaMultiDecon_two_modals property)

E

epochs (smoder.models.deconvolution.SpaMultiDecon_two_modals property)

F

feature_engineering_and_graph_build() (in module smoder.pipelines.mousebrain_h3k27ac) filter_out_low_quality_data() (in module smoder.preprocessing.rna) filter_valid_genes() (in module smoder.postprocessing.reconstruction)

forward() (smoder.postprocessing.reconstruction.DenseGCNConv method) (smoder.postprocessing.reconstruction.RNAFCModel method) (smoder.postprocessing.reconstruction.SecondModalityGCNModel method)

G

get_cell_type_proportions() (in module smoder.visualization.spatial) get_laplacian() (smoder.models.deconvolution.SpaMultiDecon_two_modals method) get_mousebrain_h3k27ac_base_config() (in module smoder.config.defaults)

get_mousebrain_h3k27ac_params() (in module smoder.config.defaults) get_spatial_hvgs_only() (in module smoder.preprocessing.rna) get_spatial_xy() (in module smoder.visualization.spatial)

H

hidden_dim (smoder.models.deconvolution.SpaMultiDecon_two_modals property)

I

init_model_and_preprocess() (in module smoder.pipelines.mousebrain_h3k27ac)

L

learning_rate (smoder.models.deconvolution.SpaMultiDecon_two_modals property) load_align_data() (in module smoder.postprocessing.reconstruction)

load_and_show_data() (in module smoder.pipelines.mousebrain_h3k27ac) lognorm_transform() (in module smoder.postprocessing.reconstruction) lsi_random_state (smoder.models.deconvolution.SpaMultiDecon_two_modals property)

M

main() (in module smoder.pipelines.mousebrain_h3k27ac) modal2_target_dim (smoder.models.deconvolution.SpaMultiDecon_two_modals property) module smoder.config.defaults smoder.models.deconvolution smoder.pipelines.mousebrain_h3k27ac smoder.postprocessing.reconstruction smoder.preprocessing.modality2 smoder.preprocessing.rna smoder.visualization.spatial

N

normalize_coords() (in module smoder.postprocessing.reconstruction)

normalize_expression_matrix() (in module smoder.preprocessing.rna) normalize_single_cell() (in module smoder.preprocessing.rna)

O

omics_reconstruct() (in module smoder.postprocessing.reconstruction)

P

pca_n_components_rna (smoder.models.deconvolution.SpaMultiDecon_two_modals property) plot_all_cell_type_proportions() (in module smoder.visualization.spatial) plot_cell_type_proportion_panel() (in module smoder.visualization.spatial) plot_embedding_spatial_clustering() (in module smoder.visualization.spatial) plot_individual_cell_type_heatmaps() (in module smoder.visualization.spatial) plot_reconstruction_heatmaps() (in module smoder.visualization.spatial) preprocess() (smoder.models.deconvolution.SpaMultiDecon_two_modals method) process_peak_data() (in module smoder.preprocessing.modality2)

process_peak_data_path() (in module smoder.preprocessing.modality2) process_single_cell() (in module smoder.preprocessing.rna) process_single_cell_path() (in module smoder.preprocessing.rna) process_spatial_adt_data() (in module smoder.preprocessing.modality2) process_spatial_adt_data_path() (in module smoder.preprocessing.modality2) process_spatial_data() (in module smoder.preprocessing.rna) process_spatial_data_path() (in module smoder.preprocessing.rna) project_coords() (in module smoder.postprocessing.reconstruction)

R

rna_run() (in module smoder.postprocessing.reconstruction)

RNAFCModel (class in smoder.postprocessing.reconstruction) run_feature_engineering_and_mapping() (smoder.models.deconvolution.SpaMultiDecon_two_modals method)

S

sanitize_filename() (in module smoder.preprocessing.rna) (in module smoder.visualization.spatial) save_results() (in module smoder.pipelines.mousebrain_h3k27ac) save_spatial_categorical() (in module smoder.visualization.spatial) save_spatial_continuous() (in module smoder.visualization.spatial) second_modality_preprocess_batch() (in module smoder.postprocessing.reconstruction) second_modality_preprocess_single() (in module smoder.postprocessing.reconstruction) second_modality_run() (in module smoder.postprocessing.reconstruction) SecondModalityGCNModel (class in smoder.postprocessing.reconstruction) seed (smoder.models.deconvolution.SpaMultiDecon_two_modals property) select_hvgs() (in module smoder.preprocessing.rna) selectInfoGenes() (in module smoder.models.deconvolution) set_analysis_params() (in module smoder.pipelines.mousebrain_h3k27ac) set_base_config() (in module smoder.pipelines.mousebrain_h3k27ac) set_nn_para() (smoder.models.deconvolution.SpaMultiDecon_two_modals method) set_random_seed() (in module smoder.postprocessing.reconstruction)

smoder.config.defaults module smoder.models.deconvolution module smoder.pipelines.mousebrain_h3k27ac module smoder.postprocessing.reconstruction module smoder.preprocessing.modality2 module smoder.preprocessing.rna module smoder.visualization.spatial module SpaMultiDecon_two_modals (class in smoder.models.deconvolution) standardize_embedding() (in module smoder.postprocessing.reconstruction)

T

train() (smoder.models.deconvolution.SpaMultiDecon_two_modals method)

train_model() (in module smoder.pipelines.mousebrain_h3k27ac)

W

weight_consistency (smoder.models.deconvolution.SpaMultiDecon_two_modals property)

weight_loss (smoder.models.deconvolution.SpaMultiDecon_two_modals property) weight_spatial (smoder.models.deconvolution.SpaMultiDecon_two_modals property)