What is scVelo used for?

scVelo is a Python-based tool used to estimate RNA velocity, allowing researchers to predict the future state of individual cells based on mRNA splicing dynamics in single-cell RNA-seq data.

Can I use scVelo alongside Scanpy?

Yes, scVelo is designed to be fully compatible with Scanpy. It uses the same AnnData structure and often utilizes Scanpy's preprocessing and clustering results as a starting point.

How does the dynamical model differ from the stochastic model?

The dynamical model fits the full splicing kinetics and is more accurate for identifying driver genes and latent time, whereas the stochastic model is faster and suitable for initial exploration.

Does this skill require specific data formats?

Yes, scVelo requires an AnnData object containing both 'spliced' and 'unspliced' count layers, typically generated by tools like velocyto, STARsolo, or alevin-fry.

scVelo RNA Velocity Analysis

Name: scVelo RNA Velocity Analysis
Author: Yezez9

byYezez9

0•

Ciencia de Datos y ML

Performs advanced RNA velocity analysis to infer cell state transitions and developmental trajectories from single-cell transcriptomics data.

The scVelo skill equips Claude with specialized knowledge for modeling RNA splicing kinetics in single-cell RNA-seq datasets. By leveraging the ratio between unspliced and spliced mRNA, it enables researchers to reconstruct developmental lineages, estimate latent time, and identify the specific driver genes behind cellular differentiation. This skill provides implementation patterns for both stochastic and dynamical modeling, integrating seamlessly with the Python single-cell ecosystem including Scanpy and AnnData to transform snapshot data into directional trajectories.

Características Principales

01Driver gene identification and velocity ranking

02Directional trajectory visualization on UMAP and t-SNE

03Stochastic and dynamical RNA velocity modeling

04Automated preprocessing and moment computation workflows

05Latent time and pseudotime estimation

060 GitHub stars

Casos de Uso

01Adding directional flow information to static single-cell clusters

02Predicting cell fate transitions in developmental biology and disease progression

03Identifying key genes driving specific cellular differentiation pathways

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent scvelo

For use in Claude.ai and ChatGPT