single-trajectory-analysis

Reproduce and extend single-trajectory analysis in OmicVerse using PAGA, Palantir, VIA, velocity coupling, and fate scoring.

• Graph-based trajectory inference with PAGA, Palantir, VIA
• Velocity coupling using scVelo and VIA
• Fate scoring via downstream notebooks
• Reproducible workflow for immune cell differentiation

• Harmonize neighbor graph parameters across methods
• Use velocity layers to refine lineage directionality
• Cross-validate pseudotime and branch probabilities
• Automated root selection in VIA with manual overrides
• Downstream fate scoring with T-cell subset mapping
• Critical parameter tuning for robustness
• Must ensure velocity layers are preserved
• Must avoid NaN values in data matrix

1. 1.Run quality control, normalization, and batch correction
2. 2.Compute PCA, neighbors, and embeddings for all methods
3. 3.Apply velocity coupling with scVelo and VIA
4. 4.Overlay and validate pseudotime from PAGA, Palantir, VIA
5. 5.Export pseudotime and fate probabilities to CSV
6. 6.Visualize and share with consistent color schemes and metadata