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 Clustering And Batch Correction With Omicverse
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in…
Install Single Cell Clustering And Batch Correction With Omicverse
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-clustering-and-batch-correction-with-omicverse -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-clustering-and-batch-correction-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-clustering .claude/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .claude/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-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 single-cell-clustering-and-batch-correction-with-omicverse -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-clustering-and-batch-correction-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-clustering .agents/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .agents/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-clustering-and-batch-correction-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-clustering .cursor/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .cursor/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-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 single-cell-clustering-and-batch-correction-with-omicverse -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-clustering-and-batch-correction-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-clustering .gemini/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .gemini/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-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-clustering-and-batch-correction-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-clustering .github/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .github/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-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-clustering-and-batch-correction-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-clustering .opencode/skills/single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-clustering into .opencode/skills/single-cell-clustering-and-batch-correction-with-omicverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 746 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in…
- Works in 11 steps: Import libraries and set plotting defaults → Load data and annotate batches → Run quality control → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Examples and References
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Single Cell Clustering And Batch Correction With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in tcluster.ipynb and tsinglebatch.ipynb.
Its SKILL.md is about 2k 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 and Jupyter notebooks. 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
- Tasks that involve Jupyter notebooks
Example prompts
- “/single-cell-clustering-and-batch-correction-with-omicverse”
Requirements
- Python 3
Workflow steps
11 steps, taken from the first numbered list in SKILL.md.
- Import libraries and set plotting defaults
- Load data and annotate batches
- Run quality control
- Preprocess and select features
- Construct neighbourhood graph and baseline clustering
- Explore advanced clustering strategies
- Evaluate clustering quality
- Embed with multiple layouts
- Perform batch correction and integration
- Benchmark integration performance
- General troubleshooting
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.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Single Cell Clustering And Batch Correction With Omicverse loads about 2k tokens when it runs. Until then it costs about 72 tokens; SKILL.md has 746 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 746 words (~2,018 tokens).
“This skill distills the single-cell tutorials t_cluster.ipynb and t_single_batch.ipynb. Use it when a user wants to preprocess an AnnData object, explore clustering alternatives (Leiden, Louvain, scICE, GMM, topic/cNMF models), and evaluate or harmonise batches with omicverse utilities.”
- name
- single-cell-clustering-and-batch-correction-with-omicverse
- title
- Single-cell clustering and batch correction with omicverse
Files
SKILL.md and 1 other file in skills/single-clustering 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 Clustering And Batch Correction 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 Clustering And Batch Correction With Omicverse this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Pixi Environment Builderxuzhougeng/wisp-science | 1k | — | ~3.7k | Automated safety check: Pass | AGPL-3.0 | |
| Check Envbrycewang-stanford/Auto-Empirical-Research-Skills | 4.6k | — | ~578 | Automated safety check: Notes | Custom licence | |
| New Notebookbrycewang-stanford/Auto-Empirical-Research-Skills | 4.6k | — | ~361 | Automated safety check: Notes | Custom licence | |
| Jupyter Notebookmicrosoft/ai-agents-for-beginners | 77k | 8 repos | ~1k | Automated safety check: Pass | Apache-2.0 | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 |
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Questions about Single Cell Clustering And Batch Correction With Omicverse
What does Single Cell Clustering And Batch Correction With Omicverse do?
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in…. Single Cell Clustering And Batch Correction With Omicverse is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.ipynb.
When should I use Single Cell Clustering And Batch Correction With Omicverse?
Single Cell Clustering And Batch Correction With Omicverse fits situations like: tasks that involve Bioinformatics; tasks that involve Jupyter notebooks.
How do I install Single Cell Clustering And Batch Correction With Omicverse in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-clustering-and-batch-correction-with-omicverse -a claude-code`. Or copy the skill folder (skills/single-clustering in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/single-cell-clustering-and-batch-correction-with-omicverse in your project. Claude Code loads it when a task matches its description.
How do I install Single Cell Clustering And Batch Correction With Omicverse in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-clustering-and-batch-correction-with-omicverse -a codex`. Or copy the skill folder (skills/single-clustering in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/single-cell-clustering-and-batch-correction-with-omicverse in your project. Codex loads it when a task matches its description.
Can I use Single Cell Clustering And Batch Correction 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-clustering-and-batch-correction-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-clustering-and-batch-correction-with-omicverse, .gemini/skills/single-cell-clustering-and-batch-correction-with-omicverse, .github/skills/single-cell-clustering-and-batch-correction-with-omicverse and .opencode/skills/single-cell-clustering-and-batch-correction-with-omicverse in your project.
What does Single Cell Clustering And Batch Correction With Omicverse need to run?
SKILL.md names no scripts, command-line tools or credentials: Single Cell Clustering And Batch Correction With Omicverse is instructions for the agent only. Our summary lists: Python 3.
Does Single Cell Clustering And Batch Correction With Omicverse access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Single Cell Clustering And Batch Correction 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 Clustering And Batch Correction With Omicverse use?
No licence was found for Single Cell Clustering And Batch Correction With Omicverse or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Single Cell Clustering And Batch Correction With Omicverse use?
About 2k tokens (SKILL.md is roughly 8.1k 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 Single Cell Clustering And Batch Correction With Omicverse?
Skills that share tags, products or a category with Single Cell Clustering And Batch Correction With Omicverse: Pixi Environment Builder (xuzhougeng/wisp-science, 1k stars), Check Env (brycewang-stanford/Auto-Empirical-Research-Skills, 4.6k stars), New Notebook (brycewang-stanford/Auto-Empirical-Research-Skills, 4.6k stars) and Jupyter Notebook (microsoft/ai-agents-for-beginners, 77k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single Cell Clustering And Batch Correction 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.