Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Agent skill
Single Cell Multi Omics Integration
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
Install Single Cell Multi Omics Integration
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-multi-omics-integration -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-multi-omics-integration --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-multiomics .claude/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .claude/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multiomicsType 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-multi-omics-integration -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-multi-omics-integration --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-multiomics .agents/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .agents/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multi-omics-integration -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-multi-omics-integration --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-multiomics .cursor/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .cursor/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multiomics--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-multi-omics-integration -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills single-cell-multi-omics-integration --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-multiomics .gemini/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .gemini/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multi-omics-integrationInstalls 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-multi-omics-integration -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-multiomics .github/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .github/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multi-omics-integration -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-multi-omics-integration --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-multiomics .opencode/skills/single-cell-multi-omics-integration && 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-multi-omics-integration" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-multiomics into .opencode/skills/single-cell-multi-omics-integration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-multi-omics-integration", 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-multi-omics-integration- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.5k tokens
- SKILL.md length
- 639 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
- Tasks that involve Bioinformatics
- SKILL.md covers MOFA on paired scRNA + scATAC…, MOFA after GLUE pairing…, SIMBA batch integration… and TOSICA reference transfer…, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Single Cell Multi Omics Integration is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
Its SKILL.md is about 1.5k 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 and AnnData. 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-multi-omics-integration”
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 Multi Omics Integration loads about 1.5k tokens when it runs. Until then it costs about 43 tokens; SKILL.md has 639 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 639 words (~1,476 tokens).
“This skill walk-through summarizes the OmicVerse notebooks that cover paired and unpaired multi-omic integration, multi-batch embedding, reference transfer, and trajectory cartography.”
- name
- single-cell-multi-omics-integration
- title
- Single-cell multi-omics integration
Files
SKILL.md and 1 other file in skills/single-multiomics 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 Multi Omics Integration 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 Multi Omics Integration this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.5k | Automated safety check: Pass | None | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 33k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| ScgptJimLiu/science-skills | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 33k | 11 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 739 | 1 repos | ~1.4k | Automated safety check: Pass | MIT |
Similar skills
Scgpt
JimLiu/science-skills
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.
PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
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…
Single-Cell Initial Analysis
LigphiDonk/Oh-my--paper
Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
Single Cell Data Prep Qc
harrisongzhang/TheVirtualBiotech
Single-cell RNA-seq data preparation and quality control pipeline.
More from FreedomIntelligence/OpenClaw-Medical-Skills
All 279 skills in this repoSingle Cell Rna Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
Differentiation Schemes
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
Fhir Developer Skill
FreedomIntelligence/OpenClaw-Medical-Skills
FHIR API development guide for building healthcare endpoints.
Linear Solvers
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure linear solvers for systems Ax=b in dense and sparse problems.
Medical Research Toolkit
FreedomIntelligence/OpenClaw-Medical-Skills
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Mesh Generation
FreedomIntelligence/OpenClaw-Medical-Skills
Plan and evaluate mesh generation for numerical simulations.
Related
Categories
Questions about Single Cell Multi Omics Integration
What does Single Cell Multi Omics Integration do?
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography. Single Cell Multi Omics Integration is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
When should I use Single Cell Multi Omics Integration?
Single Cell Multi Omics Integration fits situations like: tasks that involve Bioinformatics.
How do I install Single Cell Multi Omics Integration in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-multi-omics-integration -a claude-code`. Or copy the skill folder (skills/single-multiomics in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/single-cell-multi-omics-integration in your project. Claude Code loads it when a task matches its description.
How do I install Single Cell Multi Omics Integration in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cell-multi-omics-integration -a codex`. Or copy the skill folder (skills/single-multiomics in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/single-cell-multi-omics-integration in your project. Codex loads it when a task matches its description.
Can I use Single Cell Multi Omics Integration 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-multi-omics-integration -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-multi-omics-integration, .gemini/skills/single-cell-multi-omics-integration, .github/skills/single-cell-multi-omics-integration and .opencode/skills/single-cell-multi-omics-integration in your project.
What does Single Cell Multi Omics Integration need to run?
SKILL.md names no scripts, command-line tools or credentials: Single Cell Multi Omics Integration is instructions for the agent only.
Does Single Cell Multi Omics Integration 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 Multi Omics Integration 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 Multi Omics Integration use?
No licence was found for Single Cell Multi Omics Integration or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Single Cell Multi Omics Integration use?
About 1.5k tokens (SKILL.md is roughly 5.9k 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 Multi Omics Integration?
Skills that share tags, products or a category with Single Cell Multi Omics Integration: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Scgpt (JimLiu/science-skills, 228 stars), PyDESeq2 Differential Expression (davila7/claude-code-templates, 33k stars) and Anndata (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single Cell Multi Omics Integration?
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.