Infers cell state transitions from mRNA dynamics using scvelo and Scanpy.
npx skills add https://github.com/JosephWoodall/noosphere --skill scvelo-josephwoodall
Please help me install this Agent Skill. Skill: scvelo Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/scvelo Command: npx skills add https://github.com/JosephWoodall/noosphere --skill scvelo-josephwoodall
RNA velocity analysis with scVelo enables inference of cell state transitions from unspliced/spliced mRNA dynamics to reveal developmental trajectories and cellular futures.
Install scvelo and run a basic velocity workflow on an AnnData object with spliced and unspliced layers.
High-intent search queries and answers about installing and using this skill.
To infer RNA velocity trajectories from scRNA-seq data, use scvelo to model transcriptional kinetics from spliced and unspliced mRNA layers. This reconstructs developmental trajectories and predicts cellular state transitions within Scanpy and AnnData workflows.
RNA velocity estimation uses stochastic and dynamical models to capture transcriptional kinetics from unspliced and spliced mRNA. By analyzing these dynamics, it calculates latent time and identifies driver genes acting as key regulators of cell fate directions.
Yes, velocity graph estimation requires an AnnData object containing both spliced and unspliced mRNA layers. Standard preprocessing steps must be applied to this single-cell RNA-seq data before generating velocity graphs and trajectory visualizations.
Yes, scvelo integrates seamlessly with Scanpy and AnnData workflows to visualize latent time and cell state transitions. It generates velocity graphs that map cell fate directions directly within the Scanpy environment using matplotlib.
The best way to analyze single-cell RNA-seq transcriptional kinetics is applying scvelo's dynamical model to your AnnData object. This approach estimates RNA velocity, calculates latent time, and produces velocity graphs for mapping developmental trajectories.
yf8578Perform RNA velocity analysis on single-cell RNA-seq AnnData objects.
dralkhAnalyze RNA velocity data from single-cell transcriptomic matrices with scVelo.
tassiovaleAnalyze single-cell RNA-seq data with scvelo to infer cell state transitions and latent time.
qinyan-aiInfer RNA velocity and latent time from spliced and unspliced mRNA in AnnData objects.
