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version: "1.0.0"

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/

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