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Agent skill

Tooluniverse Spatial Omics Analysis

by wu-yc in wu-yc/LabClaw

Computational analysis framework for spatial multi-omics data integration.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Spatial Omics Analysis

skills CLI
$ npx skills add wu-yc/LabClaw --skill tooluniverse-spatial-omics-analysis -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install wu-yc/LabClaw tooluniverse-spatial-omics-analysis --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio/tooluniverse-spatial-omics-analysis .claude/skills/tooluniverse-spatial-omics-analysis && rm -rf skills-src

Use ~/.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/

Facts

Skill name
tooluniverse-spatial-omics-analysis
GitHub stars
1.1k
Used in
2 other repos
Token cost
~12k tokens
SKILL.md length
3,874 words
Files
1
Skills in repo
68
Repo updated
First seen
Licence
None found

At a glance

Computational analysis framework for spatial multi-omics data integration.

  • Works in 9 steps: Input Processing & Disambiguation… → Gene Characterization → Pathway & Functional Enrichment → …
  • Users ask about spatial transcriptomics analysis
  • SKILL.md covers When to Use This Skill, Input Parameters, Spatial Omics Integration… and Report Template, plus 6 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tooluniverse Spatial Omics Analysis is an agent skill from wu-yc/LabClaw. Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus, SLIDE-seq, etc.), performs comprehensive biological interpretation including pathway enrichment, cell-cell interaction inference, druggable target identification, immune microenvironment characterization, and multi-modal integration. Produces a detailed…

Its SKILL.md is about 12k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

  • Users ask about spatial transcriptomics analysis
  • Spatial omics interpretation
  • Tissue heterogeneity
  • Spatial gene expression patterns

Example prompts

  • “/tooluniverse-spatial-omics-analysis”

Workflow steps

9 steps, taken from the step headings in SKILL.md.

  1. Input Processing & Disambiguation (ALWAYS FIRST)
  2. Gene Characterization
  3. Pathway & Functional Enrichment
  4. Spatial Domain Characterization
  5. Cell-Cell Interaction Inference
  6. Disease & Therapeutic Context
  7. Multi-Modal Integration
  8. Immune Microenvironment (Cancer/Inflammation)
  9. Literature & Validation Context

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. 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 markdown).

    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

Tooluniverse Spatial Omics Analysis loads about 12k tokens when it runs. Until then it costs about 243 tokens; SKILL.md has 3,874 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~243
When it runs · the whole SKILL.md, loaded when a task matches
~12k

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 3,874 words (~11,562 tokens).

“Comprehensive biological interpretation of spatial omics data. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into actionable biological insights covering pathway enrichment, cell-cell interactions, druggable targets, immune microenvironment, and multi-modal integration.”

— opening of SKILL.md by wu-yc
name
tooluniverse-spatial-omics-analysis

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-spatial-omics-analysis of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in wu-yc/LabClaw, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Tooluniverse Spatial Omics Analysis 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.

Tooluniverse Spatial Omics Analysis compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tooluniverse Spatial Omics Analysis this skillwu-yc/LabClaw1.1k2 repos~12kAutomated safety check: PassNone
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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More from wu-yc/LabClaw

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  • Tooluniverse Disease Research

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  • Tooluniverse Drug Repurposing

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    Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies.

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  • Tooluniverse Expression Data Retrieval

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    Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.

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  • Tooluniverse Gene Enrichment

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    Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

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Categories

Questions about Tooluniverse Spatial Omics Analysis

What does Tooluniverse Spatial Omics Analysis do?

Computational analysis framework for spatial multi-omics data integration. Tooluniverse Spatial Omics Analysis is an agent skill from wu-yc/LabClaw. Computational analysis framework for spatial multi-omics data integration.

When should I use Tooluniverse Spatial Omics Analysis?

Tooluniverse Spatial Omics Analysis fits situations like: users ask about spatial transcriptomics analysis; spatial omics interpretation; tissue heterogeneity; spatial gene expression patterns.

How do I install Tooluniverse Spatial Omics Analysis in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-spatial-omics-analysis -a claude-code`. Or copy the skill folder (skills/bio/tooluniverse-spatial-omics-analysis in wu-yc/LabClaw) into .claude/skills/tooluniverse-spatial-omics-analysis in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse Spatial Omics Analysis in Codex?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-spatial-omics-analysis -a codex`. Or copy the skill folder (skills/bio/tooluniverse-spatial-omics-analysis in wu-yc/LabClaw) into .agents/skills/tooluniverse-spatial-omics-analysis in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse Spatial Omics Analysis 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 wu-yc/LabClaw --skill tooluniverse-spatial-omics-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tooluniverse-spatial-omics-analysis, .gemini/skills/tooluniverse-spatial-omics-analysis, .github/skills/tooluniverse-spatial-omics-analysis and .opencode/skills/tooluniverse-spatial-omics-analysis in your project.

What does Tooluniverse Spatial Omics Analysis need to run?

SKILL.md names no scripts, command-line tools or credentials: Tooluniverse Spatial Omics Analysis is instructions for the agent only.

Does Tooluniverse Spatial Omics Analysis 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 Tooluniverse Spatial Omics Analysis 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 Tooluniverse Spatial Omics Analysis use?

No licence was found for Tooluniverse Spatial Omics Analysis or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Tooluniverse Spatial Omics Analysis use?

About 12k tokens (SKILL.md is roughly 46k 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 Tooluniverse Spatial Omics Analysis?

Skills that share tags, products or a category with Tooluniverse Spatial Omics Analysis: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Spatial Omics Analysis?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

Source: wu-yc/LabClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.