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…
Agent skill
Bio Single Cell Preprocessing
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Install Bio Single Cell Preprocessing
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-preprocessing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-preprocessing --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-preprocessing .claude/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .claude/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessingType 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-preprocessing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-preprocessing --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-preprocessing .agents/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .agents/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-preprocessing --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-preprocessing .cursor/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .cursor/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessing--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-preprocessing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-preprocessing --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-preprocessing .gemini/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .gemini/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessingInstalls 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-preprocessing -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-preprocessing .github/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .github/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessing -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-preprocessing --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-preprocessing .opencode/skills/bio-single-cell-preprocessing && 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-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-preprocessing into .opencode/skills/bio-single-cell-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-preprocessing", 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-preprocessing- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2.4k tokens
- SKILL.md length
- 387 words
- Files
- 4
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
- Calculating QC metrics
- SKILL.md covers Version Compatibility, Scanpy (Python), Seurat (R) and QC Thresholds Reference, plus 2 more sections
- Runs Python and R scripts from its folder; calls pip
- Filtering cells and genes
What it does
Bio Single Cell Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calculating QC metrics, filtering cells and genes, normalizing counts, identifying highly variable genes, and scaling data. Use when filtering, normalizing, and selecting features in single-cell data.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/preprocess_scanpy.py` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics and Database schema design. It works with Scanpy and Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Calculating QC metrics
- Filtering cells and genes
- Normalizing counts
- Identifying highly variable genes
Example prompts
- “/bio-single-cell-preprocessing”
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 Preprocessing loads about 2.4k tokens when it runs. Until then it costs about 87 tokens; SKILL.md has 387 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 387 words (~2,413 tokens).
“Reference examples tested with: ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+”
- name
- bio-single-cell-preprocessing
- tool_type
- mixed
- primary_tool
- Seurat
Files
SKILL.md and 3 other files in skills/bio-single-cell-preprocessing of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/preprocess_scanpy.py
- examples/preprocess_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 7, 2026.
Compare with similar skills
Bio Single Cell Preprocessing 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 Preprocessing this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.4k | Automated safety check: Pass | None | |
| Anndatadavila7/claude-code-templates | 32k | 12 repos | ~2.5k | Automated safety check: Pass | MIT | |
| ScanpyK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~5.1k | Automated safety check: Pass | BSD-3-Clause | |
| AnndataK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.9k | Automated safety check: Notes | BSD-3-Clause | |
| Bio Geo Datamajiayu000/claude-skill-registry | 666 | 3 repos | ~4.4k | Automated safety check: Pass | MIT | |
| Bio Flow Cytometry Fcs HandlingGPTomics/bioSkills | 1.2k | 1 repos | ~2.5k | Automated safety check: Pass | MIT |
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Anndata
K-Dense-AI/scientific-agent-skills
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.
Bio Geo Data
majiayu000/claude-skill-registry
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.
Bio Flow Cytometry Fcs Handling
GPTomics/bioSkills
Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces.
Bio Single Cell Clustering
GPTomics/bioSkills
Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R).
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Related
Categories
Questions about Bio Single Cell Preprocessing
What does Bio Single Cell Preprocessing do?
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Bio Single Cell Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
When should I use Bio Single Cell Preprocessing?
Bio Single Cell Preprocessing fits situations like: calculating QC metrics; filtering cells and genes; normalizing counts; identifying highly variable genes.
How do I install Bio Single Cell Preprocessing in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-preprocessing -a claude-code`. Or copy the skill folder (skills/bio-single-cell-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-single-cell-preprocessing in your project. Claude Code loads it when a task matches its description.
How do I install Bio Single Cell Preprocessing in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-preprocessing -a codex`. Or copy the skill folder (skills/bio-single-cell-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-single-cell-preprocessing in your project. Codex loads it when a task matches its description.
Can I use Bio Single Cell Preprocessing 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-preprocessing -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-preprocessing, .gemini/skills/bio-single-cell-preprocessing, .github/skills/bio-single-cell-preprocessing and .opencode/skills/bio-single-cell-preprocessing in your project.
What does Bio Single Cell Preprocessing need to run?
Going by SKILL.md and its folder, Bio Single Cell Preprocessing 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 Preprocessing 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 Preprocessing 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 Preprocessing use?
No licence was found for Bio Single Cell Preprocessing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Single Cell Preprocessing use?
About 2.4k tokens (SKILL.md is roughly 9.7k 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 Preprocessing?
Skills that share tags, products or a category with Bio Single Cell Preprocessing: Anndata (davila7/claude-code-templates, 32k stars), Scanpy (K-Dense-AI/scientific-agent-skills, 48k stars), Anndata (K-Dense-AI/scientific-agent-skills, 48k stars) and Bio Geo Data (majiayu000/claude-skill-registry, 666 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 Preprocessing?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 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.