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…
Agent skill
Bio Single Cell Clustering
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Install Bio Single Cell Clustering
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clustering --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-single-cell-clustering .claude/skills/bio-single-cell-clustering && 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 "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .claude/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clusteringType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clustering --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-single-cell-clustering .agents/skills/bio-single-cell-clustering && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .agents/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clustering --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-single-cell-clustering .cursor/skills/bio-single-cell-clustering && 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 "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .cursor/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-single-cell-clustering--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clustering --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-single-cell-clustering .gemini/skills/bio-single-cell-clustering && 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 "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .gemini/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clusteringInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-single-cell-clustering .github/skills/bio-single-cell-clustering && 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 "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .github/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-clustering --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-single-cell-clustering .opencode/skills/bio-single-cell-clustering && 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 "bio-single-cell-clustering" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-clustering into .opencode/skills/bio-single-cell-clustering/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-clustering", 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
bio-single-cell-clustering- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 349 words
- Files
- 4
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
- Computing neighbors
- SKILL.md covers Version Compatibility, Scanpy (Python), Seurat (R) and Parameter Reference, plus 2 more sections
- Runs Python and R scripts from its folder; calls pip
- Clustering with Leiden/Louvain algorithms
What it does
Bio Single Cell Clustering is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE embeddings, and visualizing clusters. Use when performing dimensionality reduction and clustering on single-cell data.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/cluster_scanpy.py` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics. It works with UMAP, Scanpy and Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Computing neighbors
- Clustering with Leiden/Louvain algorithms
- Generating UMAP/tSNE embeddings
- Visualizing clusters
Example prompts
- “/bio-single-cell-clustering”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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
Ships script files (Python and R), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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
Bio Single Cell Clustering loads about 2k tokens when it runs. Until then it costs about 88 tokens; SKILL.md has 349 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
Without a licence we can't republish the file, so here is its outline and opening line. It has 349 words (~1,958 tokens).
“Reference examples tested with: ggplot2 3.5+, matplotlib 3.8+, scanpy 1.10+”
- name
- bio-single-cell-clustering
- tool_type
- mixed
- primary_tool
- Seurat
Files
SKILL.md and 3 other files in skills/bio-single-cell-clustering of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/cluster_scanpy.py
- examples/cluster_seurat.R
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Bio Single Cell Clustering 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 |
|---|---|---|---|---|---|---|
| Bio Single Cell Clustering this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| ScanpyK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~5.1k | Automated safety check: Pass | BSD-3-Clause | |
| Bio Single Cell ClusteringGPTomics/bioSkills | 1.2k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Scanpy Scrna Seqjaechang-hits/SciAgent-Skills | 371 | 1 repos | ~4.7k | Automated safety check: Pass | CC-BY-4.0 | |
| Harmony Batch Correctionjaechang-hits/SciAgent-Skills | 371 | 2 repos | ~5.6k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 32k | 11 repos | ~2.5k | Automated safety check: Pass | MIT |
Similar skills
Bio Single Cell Clustering
GPTomics/bioSkills
Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R).
Scanpy Scrna Seq
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scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference.
Harmony Batch Correction
jaechang-hits/SciAgent-Skills
Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills.
Anndata
davila7/claude-code-templates
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…
Anndata
K-Dense-AI/scientific-agent-skills
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.
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Related
Categories
Questions about Bio Single Cell Clustering
What does Bio Single Cell Clustering do?
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Bio Single Cell Clustering is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
When should I use Bio Single Cell Clustering?
Bio Single Cell Clustering fits situations like: computing neighbors; clustering with Leiden/Louvain algorithms; generating UMAP/tSNE embeddings; visualizing clusters.
How do I install Bio Single Cell Clustering in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a claude-code`. Or copy the skill folder (skills/bio-single-cell-clustering in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-single-cell-clustering in your project. Claude Code loads it when a task matches its description.
How do I install Bio Single Cell Clustering in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a codex`. Or copy the skill folder (skills/bio-single-cell-clustering in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-single-cell-clustering in your project. Codex loads it when a task matches its description.
Can I use Bio Single Cell Clustering 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-clustering -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-single-cell-clustering, .gemini/skills/bio-single-cell-clustering, .github/skills/bio-single-cell-clustering and .opencode/skills/bio-single-cell-clustering in your project.
What does Bio Single Cell Clustering need to run?
Going by SKILL.md and its folder, Bio Single Cell Clustering needs Python and R for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Single Cell Clustering access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Single Cell Clustering 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 Bio Single Cell Clustering use?
No licence was found for Bio Single Cell Clustering or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Single Cell Clustering use?
About 2k tokens (SKILL.md is roughly 7.8k 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 Bio Single Cell Clustering?
Skills that share tags, products or a category with Bio Single Cell Clustering: Scanpy (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Single Cell Clustering (GPTomics/bioSkills, 1.2k stars), Scanpy Scrna Seq (jaechang-hits/SciAgent-Skills, 371 stars) and Harmony Batch Correction (jaechang-hits/SciAgent-Skills, 371 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Single Cell Clustering?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.