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Cell direction velocity analyst
Give it single-cell counts with spliced reads. Get cell direction arrows, timing and the genes that drive them.
Cell direction velocity analyst is a free AI skill for the job "Research a topic properly". Give the instructions to an AI assistant that supports the required files and tools, then review its output.
Free · No account · MIT licence · Made by K-Dense · Level: expert
Made by K-Dense. See the original on GitHub; we copied it as it is, with its licence.
What it does
Single-cell data tells you which way cells seem to be heading, how far along they are, and which genes push them. Give it counts with spliced and unspliced reads, and you get arrows on the cell map, a timeline for each cell, and ranked driver genes. The skill uses scVelo to estimate how expression is changing from the balance of spliced and unspliced reads. It supports a steady-state model and a dynamical model with latent time, and draws gene phase plots. It is strict about meaning: the arrows are model estimates, not observed movement or proof of cell fate. It works in an isolated Python setup and needs no API key.
You give it
- A single-cell file with spliced and unspliced counts
- Cell type labels and a cell map embedding
- Python set up with scVelo
- Genes of interest (optional)
You get
- Velocity arrows on a cell map
- A latent time value per cell
- Ranked driver genes
- Phase portraits for chosen genes
- Notes on what the results do not prove
Use it when
- You have single-cell data and want to see the direction of cell change.
- You need the genes that drive a branching path.
- You want a pseudo-time order for cells in a trajectory.
- You are checking if a model fits before trusting its arrows.
How to use it
- Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
- Ask for the job in your own words. Your AI opens the skill when it fits.
- It works best when your AI can run code.