CoxFormer
Tutorials
Co-expression Completion Tutorial
1. Import Dependencies
2. Configuration
3. Directory Setup & Device Initialization
4. Data Loading & Graph Construction
5. Data Splitting
6. Model & Trainer Initialization
7. Training Setup
8. Training Loop
9. Test Evaluation
10. Visualization
11. Full Inference
12. Save Intermediate Results
13. Generate Full Co-expression Matrix
14. Analysis Report & Performance Summary
15. File Validation
16. Summary
Celltype Annotation Tutorial
Gene Expression Prediction Tutorial
0. Configuration
1. Metric computation (optional)
2. Cross-dataset benchmarking
3. Gene-level spatial visualization
Gene Activity Score Prediction Tutorial
0. Configuration
1. Load ground truth and imputed matrices
1.1 Metric computation
1.2 Radar summary of metrics
2 Selected genes spatial heatmap plot
3. Visualize spatial ATAC clusters
4. Plot DEG of defined cluster
Super Resolution Enhancement Tutorial
0. Configuration
1. Pixel-level evaluation
2. Gene-level spatial maps (aligned Xenium panel)
2.1 Compared with iStar
2.2 Compared with Groundtruth (Zero-shot performance)
3. Pixel-level clustering and spatial heatmaps
3.1 Clustering on COPT prediction
3.2 Clustering on iStar prediction
4. Cell–cell communication analysis (LIANA + spatial context)
4.1 Run CCC inference
4.2 Dotplots for ligand–receptor interactions
4.4 Spatial NMF visualization
Pathological Region Detection Tutorial
0. Configuration
1. Load ground truth and imputed matrices
2. Abnormal detection across methods
3. Evaluate abnormal detection performance across datasets
3.1 Barplots (mean ± std)
3.2 ROC plots (mean ROC across datasets)
3.3 Abnormal-region spatial plots
3.4 Abnormal-region UMAP plots
4 Selected marker genes spatial heatmap plot
5 Selected housekeeping genes spatial heatmap plot
6 GO enrichment analysis
7 Supplementary
CoxFormer
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