Pixi Environment Builder
xuzhougeng/wisp-science
A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…
Agent skill
Single Cell Annotation Skills With Omicverse
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
Install Single Cell Annotation Skills With Omicverse
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-annotation-skills-with-omicverse -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-annotation-skills-with-omicverse --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/single-annotation .claude/skills/single-cell-annotation-skills-with-omicverse && 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 "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .claude/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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/single-annotationType 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 single-cell-annotation-skills-with-omicverse -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-annotation-skills-with-omicverse --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/single-annotation .agents/skills/single-cell-annotation-skills-with-omicverse && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .agents/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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 single-cell-annotation-skills-with-omicverse -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-annotation-skills-with-omicverse --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/single-annotation .cursor/skills/single-cell-annotation-skills-with-omicverse && 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 "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .cursor/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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/single-annotation--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 single-cell-annotation-skills-with-omicverse -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-annotation-skills-with-omicverse --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/single-annotation .gemini/skills/single-cell-annotation-skills-with-omicverse && 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 "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .gemini/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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 single-cell-annotation-skills-with-omicverseInstalls 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 single-cell-annotation-skills-with-omicverse -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/single-annotation .github/skills/single-cell-annotation-skills-with-omicverse && 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 "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .github/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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 single-cell-annotation-skills-with-omicverse -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 single-cell-annotation-skills-with-omicverse --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/single-annotation .opencode/skills/single-cell-annotation-skills-with-omicverse && 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 "single-cell-annotation-skills-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-annotation into .opencode/skills/single-cell-annotation-skills-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation-skills-with-omicverse", 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
single-cell-annotation-skills-with-omicverse- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~3.1k tokens
- SKILL.md length
- 936 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
- Works in 6 steps: SCSA automated cluster annotation → MetaTiME tumour microenvironment states → CellVote consensus labelling → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Critical API Reference - EXACT… and Examples, plus 1 more section
- Reaches figshare.com; needs AGI_API_KEY
What it does
Single Cell Annotation Skills With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
Its SKILL.md is about 3.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `reference.md`).
It sits in Research & Science, covering Bioinformatics. It works with Jupyter. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/single-cell-annotation-skills-with-omicverse”
Requirements
- Python 3
- A credential in AGI_API_KEY
Workflow steps
6 steps, taken from the first numbered list in SKILL.md.
- SCSA automated cluster annotation
- MetaTiME tumour microenvironment states
- CellVote consensus labelling
- CellMatch ontology mapping
- GPTAnno LLM-powered annotation
- Weighted KNN annotation transfer
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
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
figshare.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
AGI_API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Single Cell Annotation Skills With Omicverse loads about 3.1k tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 936 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 936 words (~3,106 tokens).
“Use this skill to reproduce and adapt the single-cell annotation playbook captured in omicverse tutorials: SCSA t_cellanno.ipynb, MetaTiME t_metatime.ipynb, CellVote t_cellvote.md & t_cellvote_pbmc3k.ipynb, CellMatch t_cellmatch.ipynb, GPTAnno t_gptanno.ipynb, and label transfer t_anno_trans.ipynb. Each section below highlights required inputs, training/inference steps, and…”
- name
- single-cell-annotation-skills-with-omicverse
- title
- Single-cell annotation skills with omicverse
Files
SKILL.md and 1 other file in skills/single-annotation of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- reference.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
Single Cell Annotation Skills With Omicverse 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 |
|---|---|---|---|---|---|---|
| Single Cell Annotation Skills With Omicverse this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~3.1k | Automated safety check: Pass | None | |
| Pixi Environment Builderxuzhougeng/wisp-science | 1k | — | ~3.7k | Automated safety check: Pass | AGPL-3.0 | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT |
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Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Clinvar Database
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A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
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Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
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Related
Works with
Categories
Questions about Single Cell Annotation Skills With Omicverse
What does Single Cell Annotation Skills With Omicverse do?
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities. Single Cell Annotation Skills With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
When should I use Single Cell Annotation Skills With Omicverse?
Single Cell Annotation Skills With Omicverse fits situations like: tasks that involve Bioinformatics.
How do I install Single Cell Annotation Skills With Omicverse in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-annotation-skills-with-omicverse -a claude-code`. Or copy the skill folder (skills/single-annotation in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/single-cell-annotation-skills-with-omicverse in your project. Claude Code loads it when a task matches its description.
How do I install Single Cell Annotation Skills With Omicverse in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-annotation-skills-with-omicverse -a codex`. Or copy the skill folder (skills/single-annotation in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/single-cell-annotation-skills-with-omicverse in your project. Codex loads it when a task matches its description.
Can I use Single Cell Annotation Skills With Omicverse 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 single-cell-annotation-skills-with-omicverse -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/single-cell-annotation-skills-with-omicverse, .gemini/skills/single-cell-annotation-skills-with-omicverse, .github/skills/single-cell-annotation-skills-with-omicverse and .opencode/skills/single-cell-annotation-skills-with-omicverse in your project.
What does Single Cell Annotation Skills With Omicverse need to run?
Going by SKILL.md and its folder, Single Cell Annotation Skills With Omicverse needs credentials named AGI_API_KEY. Our summary lists: Python 3; A credential in AGI_API_KEY.
Does Single Cell Annotation Skills With Omicverse access the network?
SKILL.md names 1 domain. In commands or code: figshare.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Single Cell Annotation Skills With Omicverse 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 Single Cell Annotation Skills With Omicverse use?
No licence was found for Single Cell Annotation Skills With Omicverse or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Single Cell Annotation Skills With Omicverse use?
About 3.1k tokens (SKILL.md is roughly 12k 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 Single Cell Annotation Skills With Omicverse?
Skills that share tags, products or a category with Single Cell Annotation Skills With Omicverse: Pixi Environment Builder (xuzhougeng/wisp-science, 1k stars), Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Clinvar Database (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single Cell Annotation Skills With Omicverse?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 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.