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Agent skill

Tooluniverse Spatial Transcriptomics

by wu-yc in wu-yc/LabClaw

Analyze spatial transcriptomics data to map gene expression in tissue architecture.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Spatial Transcriptomics

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

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

GitHub CLI
$ gh skill install wu-yc/LabClaw tooluniverse-spatial-transcriptomics --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-transcriptomics .claude/skills/tooluniverse-spatial-transcriptomics && 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-transcriptomics
GitHub stars
1.1k
Used in
3 other repos
Token cost
~6k tokens
SKILL.md length
766 words
Files
1
Skills in repo
65
Repo updated
First seen
Licence
None found

At a glance

Analyze spatial transcriptomics data to map gene expression in tissue architecture.

  • Works in 8 steps: Data Import & Quality Control → Preprocessing & Normalization → Spatial Clustering → …
  • Analyzing spatial transcriptomics datasets
  • SKILL.md covers When to Use This Skill, Core Capabilities, Workflow Overview and Phase Details, plus 5 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tooluniverse Spatial Transcriptomics is an agent skill from wu-yc/LabClaw. Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain identification, cell-cell proximity analysis, spatial gene expression patterns, tissue architecture mapping, and integration with single-cell data. Use when analyzing spatial transcriptomics datasets, studying tissue organization, identifying spatial expression patterns, mapping cell-cell interactions in tissue…

Its SKILL.md is about 6k 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

  • Analyzing spatial transcriptomics datasets
  • Studying tissue organization
  • Identifying spatial expression patterns
  • Mapping cell-cell interactions in tissue context

Example prompts

  • “/tooluniverse-spatial-transcriptomics”

Requirements

  • Python 3

Workflow steps

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

  1. Data Import & Quality Control
  2. Preprocessing & Normalization
  3. Spatial Clustering
  4. Spatially Variable Genes
  5. Neighborhood Analysis
  6. Integration with Single-Cell RNA-seq
  7. Spatial Cell Communication
  8. Spatial Report Generation

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 python and markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • doi.org
    • 10xgenomics.com

    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 Transcriptomics loads about 6k tokens when it runs. Until then it costs about 175 tokens; SKILL.md has 766 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~175
When it runs · the whole SKILL.md, loaded when a task matches
~6k

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 766 words (~5,976 tokens).

“Comprehensive analysis of spatially-resolved transcriptomics data to understand gene expression patterns in tissue architecture context. Combines expression profiling with spatial coordinates to reveal tissue organization, cell-cell interactions, and spatially variable genes.”

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

Read the full SKILL.md on GitHub

Files

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

Open the folder on GitHubat commit df37802

Used in 3 other repositories

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 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 Transcriptomics 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 Transcriptomics compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tooluniverse Spatial Transcriptomics this skillwu-yc/LabClaw1.1k3 repos~6kAutomated safety check: PassNone
Dbsnp Databasegoogle-deepmind/science-skills3.2k3 repos~3.4kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Tooluniverse Spatial Transcriptomics

What does Tooluniverse Spatial Transcriptomics do?

Analyze spatial transcriptomics data to map gene expression in tissue architecture. Tooluniverse Spatial Transcriptomics is an agent skill from wu-yc/LabClaw. Analyze spatial transcriptomics data to map gene expression in tissue architecture.

When should I use Tooluniverse Spatial Transcriptomics?

Tooluniverse Spatial Transcriptomics fits situations like: analyzing spatial transcriptomics datasets; studying tissue organization; identifying spatial expression patterns; mapping cell-cell interactions in tissue context.

How do I install Tooluniverse Spatial Transcriptomics in Claude Code?

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

How do I install Tooluniverse Spatial Transcriptomics in Codex?

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

Can I use Tooluniverse Spatial Transcriptomics 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-transcriptomics -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-transcriptomics, .gemini/skills/tooluniverse-spatial-transcriptomics, .github/skills/tooluniverse-spatial-transcriptomics and .opencode/skills/tooluniverse-spatial-transcriptomics in your project.

What does Tooluniverse Spatial Transcriptomics need to run?

SKILL.md names no scripts, command-line tools or credentials: Tooluniverse Spatial Transcriptomics is instructions for the agent only. Our summary lists: Python 3.

Does Tooluniverse Spatial Transcriptomics access the network?

SKILL.md names 2 domains. As links in the text: doi.org and 10xgenomics.com. This is read from the text; nothing was executed.

Is Tooluniverse Spatial Transcriptomics 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 Transcriptomics use?

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

How many tokens does Tooluniverse Spatial Transcriptomics use?

About 6k tokens (SKILL.md is roughly 24k 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 Transcriptomics?

Skills that share tags, products or a category with Tooluniverse Spatial Transcriptomics: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (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 Tooluniverse Spatial Transcriptomics?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,054 GitHub stars. The repository holds 65 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.