Tutorials

This section provides step-by-step tutorials for running SMODER and visualizing representative results.

Tutorial pages

• 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
  • Next steps
• SMODER Tutorial 02: Mouse Brain H3K27ac Result Visualization
  • What is spatial_decon_result.h5ad?
  • Load the SMODER result
  • Plot cell-type proportion heatmaps
  • Plot spatial clusters from learned embeddings
  • Reconstruct denoised RNA marker expression
  • Reconstruct denoised gene-level epigenomic signals
  • Complete plotting script
  • Representative results
• SMODER Tutorial 03: Simulated Human Melanoma Result Visualization
  • What is spatial_decon_result.h5ad?
  • Load the SMODER result
  • Extract spatial coordinates and proportions
  • Plot proportion heatmaps
  • Complete plotting script
  • Representative results
  • Notes
• SMODER Tutorial 04: HBC Result Visualization
  • What is spatial_decon_result.h5ad?
  • Load the SMODER result
  • Plot cell-type proportion heatmaps
  • Plot spatial clusters from learned embeddings
  • Reconstruct denoised RNA marker expression
  • Reconstruct denoised ADT marker signals
  • Complete plotting script
  • Representative results