scvelo - RNA Velocity Analysis for Single-Cell Data
Estimate cell state transitions from unspliced/spliced mRNA dynamics in single-cell RNA-seq data
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- load data
- filter and normalize
- compute moments
- estimate velocity
- compute velocity graph
- recover dynamics
- compute latent time
- rank velocity genes
- compute velocity confidence
- compute velocity pseudotime
- plot velocity embedding
- plot velocity stream
- compute PAGA graph
- plot phase portraits
- compute transition probabilities
Inputs
- count matrices
- spliced RNA
- unspliced RNA
- loom files
- AnnData object
Outputs
- velocity vectors
- velocity graph
- latent time
- velocity pseudotime
- velocity confidence
- ranked driver genes
- PAGA graph
- velocity plots
Requirements
- Python environment
- scvelo package
- scanpy package
- spliced and unspliced RNA data
- UMAP coordinates