SMODER

Contents:

  • Installation
    • Requirements
    • Install from PyPI
    • Install from GitHub
    • Create a Python environment
    • Current recommended execution method
    • Data preparation
  • Data
    • Required input files
    • Example directory layout
    • How to obtain the data
    • How to prepare data
    • Example
    • Notes
  • Tutorials
    • SMODER Tutorial 01: Mouse Brain H3K27ac Quick Start
      • Before you begin
      • Step 1. Define tutorial settings
      • Step 2. Review configuration
      • Step 3. Check required input files
      • Step 4. Load input data
      • Step 5. Initialize the model and preprocess the data
      • Step 6. Perform feature engineering and graph construction
      • Step 7. Optional model training
      • Step 8. Save results
      • Step 9. Inspect output directory
      • Step 10. Preview the cell type proportions
      • Step 11. Inspect result object metadata
      • Summary
    • Result visualization and postprocessing
      • Loading a SMODER result
      • Plotting cell-type proportion heatmaps
      • Plotting all cell types
      • Plotting embedding-based spatial clusters
      • Reconstructing denoised RNA expression
      • Reconstructing second-modality signals
      • Plotting reconstructed heatmaps
      • Notes
  • Results
    • Simulated human melanoma dataset
      • Cell-type proportion heatmaps
    • Mouse brain RNA + H3K27ac peak example
      • Training loss
      • Cell-type proportion heatmaps
      • Denoised RNA gene expression
      • Denoised gene-level epigenomic signal
      • Spatial clustering based on learned embeddings
    • Human breast cancer RNA + ADT example
      • Cell-type proportion heatmaps
      • Denoised RNA gene expression
      • Denoised ADT marker signal
      • Spatial clustering based on learned embeddings
  • API Reference
    • Core model
      • 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()
    • Pipelines
      • 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()
    • Preprocessing
      • RNA preprocessing
        • 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()
      • Second-modality preprocessing
        • clr_normalization()
        • process_spatial_adt_data()
        • process_spatial_adt_data_path()
        • process_peak_data()
        • process_peak_data_path()
    • Postprocessing
      • Reconstruction
        • 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()
    • Visualization
      • Spatial visualization
        • get_spatial_xy()
        • save_spatial_continuous()
        • save_spatial_categorical()
        • get_cell_type_proportions()
        • sanitize_filename()
        • plot_cell_type_proportion_panel()
        • plot_all_cell_type_proportions()
        • plot_individual_cell_type_heatmaps()
        • plot_embedding_spatial_clustering()
        • plot_reconstruction_heatmaps()
    • Configuration
      • get_mousebrain_h3k27ac_base_config()
      • get_mousebrain_h3k27ac_params()
  • SMODER modules
    • omics_reconstruct()
    • get_cell_type_proportions()
    • plot_all_cell_type_proportions()
    • plot_cell_type_proportion_panel()
    • plot_embedding_spatial_clustering()
    • plot_reconstruction_heatmaps()
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