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 Data Io
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python).
Install Bio Single Cell Data Io
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-data-io -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-data-io --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-data-io .claude/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .claude/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-ioType 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-data-io -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-data-io --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-data-io .agents/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .agents/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-io -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-data-io --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-data-io .cursor/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .cursor/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-io--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-data-io -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-single-cell-data-io --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-data-io .gemini/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .gemini/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-ioInstalls 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-data-io -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-data-io .github/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .github/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-io -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-data-io --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-data-io .opencode/skills/bio-single-cell-data-io && 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-data-io" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io into .opencode/skills/bio-single-cell-data-io/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-single-cell-data-io", 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-data-io- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 314 words
- Files
- 4
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python).
- Loading 10X Genomics data
- SKILL.md covers Version Compatibility, Scanpy (Python), Seurat (R) and Format Conversion, plus 2 more sections
- Runs Python and R scripts from its folder; calls pip
- Importing/exporting h5ad and RDS files
What it does
Bio Single Cell Data Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data formats.
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/load_10x_scanpy.py` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics. It works with AnnData, Scanpy and Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Loading 10X Genomics data
- Importing/exporting h5ad and RDS files
- Creating Seurat objects and AnnData objects
- Converting between formats
Example prompts
- “/bio-single-cell-data-io”
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 Data Io loads about 2k tokens when it runs. Until then it costs about 82 tokens; SKILL.md has 314 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 314 words (~1,960 tokens).
“Reference examples tested with: Cell Ranger 8.0+, anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+”
- name
- bio-single-cell-data-io
- tool_type
- mixed
- primary_tool
- Seurat
Files
SKILL.md and 3 other files in skills/bio-single-cell-data-io of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/load_10x_scanpy.py
- examples/load_10x_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 Data Io 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 Data Io this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | 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 Flow Cytometry Fcs HandlingGPTomics/bioSkills | 1.2k | 1 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Bio Expression Matrix Sparse HandlingGPTomics/bioSkills | 1.2k | 1 repos | ~5.6k | Automated safety check: Pass | MIT |
Similar skills
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…
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 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 Expression Matrix Sparse Handling
GPTomics/bioSkills
Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…
Muon Multiomics Singlecell
jaechang-hits/SciAgent-Skills
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Related
Categories
Questions about Bio Single Cell Data Io
What does Bio Single Cell Data Io do?
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Bio Single Cell Data Io is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python).
When should I use Bio Single Cell Data Io?
Bio Single Cell Data Io fits situations like: loading 10X Genomics data; importing/exporting h5ad and RDS files; creating Seurat objects and AnnData objects; converting between formats.
How do I install Bio Single Cell Data Io in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-data-io -a claude-code`. Or copy the skill folder (skills/bio-single-cell-data-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-single-cell-data-io in your project. Claude Code loads it when a task matches its description.
How do I install Bio Single Cell Data Io in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-data-io -a codex`. Or copy the skill folder (skills/bio-single-cell-data-io in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-single-cell-data-io in your project. Codex loads it when a task matches its description.
Can I use Bio Single Cell Data Io 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-data-io -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-data-io, .gemini/skills/bio-single-cell-data-io, .github/skills/bio-single-cell-data-io and .opencode/skills/bio-single-cell-data-io in your project.
What does Bio Single Cell Data Io need to run?
Going by SKILL.md and its folder, Bio Single Cell Data Io 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 Data Io 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 Data Io 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 Data Io use?
No licence was found for Bio Single Cell Data Io or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Single Cell Data Io 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 Data Io?
Skills that share tags, products or a category with Bio Single Cell Data Io: 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 Flow Cytometry Fcs Handling (GPTomics/bioSkills, 1.2k 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 Data Io?
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.