scvelo

name	scvelo
description	RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
license	BSD-3-Clause
tags	["scientific-skills","scvelo","scanpy","bioinformatics"]
metadata	{"skill-author":"Kuan-lin Huang"}

----|-----|-------------| | adata.layers | velocity | RNA velocity per gene per cell | | adata.layers | fit_t | Fitted latent time per gene per cell | | adata.obsm | velocity_umap | 2D velocity vectors on UMAP | | adata.obs | velocity_pseudotime | Pseudotime from velocity | | adata.obs | latent_time | Latent time from dynamical model | | adata.obs | velocity_length | Speed of each cell | | adata.obs | velocity_confidence | Confidence score per cell | | adata.var | fit_likelihood | Gene-level model fit quality | | adata.var | fit_alpha | Transcription rate | | adata.var | fit_beta | Splicing rate | | adata.var | fit_gamma | Degradation rate | | adata.uns | velocity_graph | Cell-cell transition probability matrix |

Velocity Models Comparison

Model	Speed	Accuracy	When to Use
stochastic	Fast	Moderate	Exploratory; large datasets
deterministic	Medium	Moderate	Simple linear kinetics
dynamical	Slow	High	Publication-quality; identifies driver genes

Best Practices

• Start with stochastic mode for exploration; switch to dynamical for final analysis
• Need good coverage of unspliced reads: Short reads (< 100 bp) may miss intron coverage
• Minimum 2,000 cells: RNA velocity is noisy with fewer cells
• Velocity should be coherent: Arrows should follow known biology; randomness indicates issues
• k-NN bandwidth matters: Too few neighbors → noisy velocity; too many → oversmoothed
• Sanity check: Root cells (progenitors) should have high unspliced/spliced ratios for marker genes
• Dynamical model requires distinct kinetic states: Works best for clear differentiation processes

Troubleshooting

Problem	Solution
Missing unspliced layer	Re-run velocyto or use STARsolo with --soloFeatures Gene Velocyto
Very few velocity genes	Lower min_shared_counts; check sequencing depth
Random-looking arrows	Try different n_neighbors or velocity model
Memory error with dynamical	Set n_jobs=1; reduce n_top_genes
Negative velocity everywhere	Check that spliced/unspliced layers are not swapped

Additional Resources

• scVelo documentation: https://scvelo.readthedocs.io/
• Tutorial notebooks: https://scvelo.readthedocs.io/tutorials/
• GitHub: https://github.com/theislab/scvelo
• Paper: Bergen V et al. (2020) Nature Biotechnology. PMID: 32747759
• velocyto (preprocessing): http://velocyto.org/
• CellRank (fate prediction, extends scVelo): https://cellrank.readthedocs.io/
• dynamo (metabolic labeling alternative): https://dynamo-release.readthedocs.io/