Scanpy
K-Dense-AI/scientific-agent-skills
Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…
RNA velocity analysis with scVelo. An agent skill from lamm-mit/scienceclaw.
Install Scvelo
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install lamm-mit/scienceclaw scvelo --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/scvelo .claude/skills/scvelo && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .claude/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/scveloType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install lamm-mit/scienceclaw scvelo --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/scvelo .agents/skills/scvelo && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .agents/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install lamm-mit/scienceclaw scvelo --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/scvelo .cursor/skills/scvelo && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .cursor/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/scvelo--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install lamm-mit/scienceclaw scvelo --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/scvelo .gemini/skills/scvelo && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .gemini/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install lamm-mit/scienceclaw scveloInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/scvelo .github/skills/scvelo && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .github/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lamm-mit/scienceclaw --skill scvelo -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install lamm-mit/scienceclaw scvelo --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/scvelo .opencode/skills/scvelo && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "scvelo" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/scvelo into .opencode/skills/scvelo/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scvelo", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
scvelo- GitHub stars
- 244
- Used in
- 4 other repos
- Token cost
- ~524 tokens
- SKILL.md length
- 202 words
- Files
- 1
- Skills in repo
- 86
- Repo updated
- First seen
- Licence
- BSD-3-Clause
At a glance
RNA velocity analysis with scVelo. An agent skill from lamm-mit/scienceclaw.
- Works in 5 steps: Velocity estimation - Compute RNA… → Trajectory inference - Reconstruct… → Latent time assignment - Order cells… → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Core Capabilities, Key Workflows and Best Practices
- Calls pip
What it does
Scvelo is an agent skill from lamm-mit/scienceclaw. 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.
Its SKILL.md is about 520 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. It works with Scanpy and scvi-tools. The licence is BSD-3-Clause.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/scvelo”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Velocity estimation - Compute RNA velocity vectors for each cell
- Trajectory inference - Reconstruct developmental paths and cell fate transitions
- Latent time assignment - Order cells along developmental/differentiation timelines
- Driver gene identification - Detect genes driving state transitions
- Gene dynamics modeling - Model transcriptional kinetics (unspliced/spliced ratios)
What it can do on your machine
Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
scvelo.readthedocs.iogithub.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Scvelo loads about 524 tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 202 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its BSD-3-Clause licence (© lamm-mit). 202 words, ~524 tokens.
Download SKILL.mdSave it as
.claude/skills/scvelo/SKILL.md (or your agent's skills folder).- 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
- metadata.skill-author
- Kuan-lin Huang
scVelo — RNA Velocity Analysis
Overview
scVelo is the leading Python package for RNA velocity analysis in single-cell RNA-seq data. It infers cell state transitions by modeling the kinetics of mRNA splicing — using the ratio of unspliced (pre-mRNA) to spliced (mature mRNA) abundances to determine whether a gene is being upregulated or downregulated in each cell. This allows reconstruction of developmental trajectories and identification of cell fate decisions without requiring time-course data.
Installation: pip install scvelo
Key resources:
- Documentation: https://scvelo.readthedocs.io/
- GitHub: https://github.com/theislab/scvelo
- Paper: Bergen et al. (2020) Nature Biotechnology. PMID: 32747759
Core Capabilities
- Velocity estimation - Compute RNA velocity vectors for each cell
- Trajectory inference - Reconstruct developmental paths and cell fate transitions
- Latent time assignment - Order cells along developmental/differentiation timelines
- Driver gene identification - Detect genes driving state transitions
- Gene dynamics modeling - Model transcriptional kinetics (unspliced/spliced ratios)
Key Workflows
- Developmental trajectory reconstruction from time-series scRNA-seq
- Cell fate decision point identification
- Pseudo-temporal ordering of cells without explicit timing
- Key gene discovery in differentiation processes
- Validation of developmental hypotheses
Best Practices
The resource recommends ensuring quality QC of spliced/unspliced counts, using stochastic models for high-noise datasets, validating velocity vectors with known developmental markers, and integrating trajectory inference with spatial transcriptomics for context.
© lamm-mit, BSD-3-Clause. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/scvelo of lamm-mit/scienceclaw.
Open the folder on GitHubat commit ab9aba1
Used in 4 other repositories
We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 4 other GitHub owners. This page covers the copy in lamm-mit/scienceclaw, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Scvelo next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Scvelo this skilllamm-mit/scienceclaw | 244 | 4 repos | ~524 | Automated safety check: Pass | BSD-3-Clause | |
| ScanpyK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~5.1k | Automated safety check: Pass | BSD-3-Clause | |
| Cellxgene CensusK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.4k | Automated safety check: Notes | MIT | |
| Scvi ToolsK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.6k | Automated safety check: Pass | BSD-3-Clause | |
| Scvi ToolsJimLiu/science-skills | 227 | 4 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| AnndataK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.9k | Automated safety check: Notes | BSD-3-Clause |
Similar skills
Cellxgene Census
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Scvi Tools
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Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression.
Scvi Tools
JimLiu/science-skills
Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression.
Anndata
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Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.
Anndata Data Structure
jaechang-hits/SciAgent-Skills
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Related
Works with
Categories
Questions about Scvelo
What does Scvelo do?
RNA velocity analysis with scVelo. An agent skill from lamm-mit/scienceclaw. Scvelo is an agent skill from lamm-mit/scienceclaw. RNA velocity analysis with scVelo.
When should I use Scvelo?
Scvelo fits situations like: tasks that involve Bioinformatics.
How do I install Scvelo in Claude Code?
Run `npx skills add lamm-mit/scienceclaw --skill scvelo -a claude-code`. Or copy the skill folder (skills/scvelo in lamm-mit/scienceclaw) into .claude/skills/scvelo in your project. Claude Code loads it when a task matches its description.
How do I install Scvelo in Codex?
Run `npx skills add lamm-mit/scienceclaw --skill scvelo -a codex`. Or copy the skill folder (skills/scvelo in lamm-mit/scienceclaw) into .agents/skills/scvelo in your project. Codex loads it when a task matches its description.
Can I use Scvelo in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill scvelo -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scvelo, .gemini/skills/scvelo, .github/skills/scvelo and .opencode/skills/scvelo in your project.
What does Scvelo need to run?
Going by SKILL.md and its folder, Scvelo needs the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Scvelo access the network?
SKILL.md names 2 domains. As links in the text: scvelo.readthedocs.io and github.com. This is read from the text; nothing was executed.
Is Scvelo safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Scvelo use?
Scvelo is published under the BSD-3-Clause licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Scvelo use?
About 524 tokens (SKILL.md is roughly 2.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Scvelo?
Skills that share tags, products or a category with Scvelo: Scanpy (K-Dense-AI/scientific-agent-skills, 48k stars), Cellxgene Census (K-Dense-AI/scientific-agent-skills, 48k stars), Scvi Tools (K-Dense-AI/scientific-agent-skills, 48k stars) and Scvi Tools (JimLiu/science-skills, 227 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Scvelo?
lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 86 skills in this directory. The repository was last updated on August 21, 2026.
Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.