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Agent skill

Tooluniverse Rnaseq Deseq2

by wu-yc in wu-yc/LabClaw

Production-ready RNA-seq differential expression analysis using PyDESeq2.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Rnaseq Deseq2

skills CLI
$ npx skills add wu-yc/LabClaw --skill tooluniverse-rnaseq-deseq2 -a claude-code

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

GitHub CLI
$ gh skill install wu-yc/LabClaw tooluniverse-rnaseq-deseq2 --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-rnaseq-deseq2 .claude/skills/tooluniverse-rnaseq-deseq2 && 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-rnaseq-deseq2
GitHub stars
1.1k
Used in
2 other repos
Token cost
~4.5k tokens
SKILL.md length
1,205 words
Files
1
Skills in repo
68
Repo updated
First seen
Licence
None found

At a glance

Production-ready RNA-seq differential expression analysis using PyDESeq2.

  • Works in 9 steps: Question Parsing → 5: Design Formula Decision Tree ⚠️… → Data Loading & Validation → …
  • Analyzing RNA-seq count matrices
  • SKILL.md covers Core Principles, When to Use This Skill, Required Packages and Analysis Workflow, plus 7 more sections
  • Calls pip

What it does

Tooluniverse Rnaseq Deseq2 is an agent skill from wu-yc/LabClaw. Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering. Handles multi-factor designs, multiple contrasts, batch effects, and integrates with gene enrichment (gseapy) and ToolUniverse annotation tools (UniProt, Ensembl, OpenTargets). Supports CSV/TSV/H5AD input formats and any organism. Use when analyzing RNA-seq count matrices, identifying DEGs, performing differential expression with…

Its SKILL.md is about 4.5k 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, CSV and tabular files and Database schema design. It works with Ensembl and UniProt. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

  • Analyzing RNA-seq count matrices
  • Identifying DEGs
  • Performing differential expression with statistical rigor
  • Answering questions about gene expression changes

Example prompts

  • “/tooluniverse-rnaseq-deseq2”

Requirements

  • Python 3

Workflow steps

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

  1. Question Parsing
  2. 5: Design Formula Decision Tree ⚠️ CRITICAL
  3. Data Loading & Validation
  4. 5: Inspect Metadata Structure ⚠️ REQUIRED
  5. Run PyDESeq2
  6. Filter Results
  7. Dispersion Analysis (if asked)
  8. Enrichment Analysis (optional)
  9. Gene Annotation with ToolUniverse (optional)

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

    Shell commands in SKILL.md call:

    • pip

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

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    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 Rnaseq Deseq2 loads about 4.5k tokens when it runs. Until then it costs about 153 tokens; SKILL.md has 1,205 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~153
When it runs · the whole SKILL.md, loaded when a task matches
~4.5k

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 1,205 words (~4,451 tokens).

“Comprehensive differential expression analysis of RNA-seq count data using PyDESeq2, with integrated enrichment analysis (gseapy) and gene annotation via ToolUniverse.”

— opening of SKILL.md by wu-yc
name
tooluniverse-rnaseq-deseq2

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-rnaseq-deseq2 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 Rnaseq Deseq2 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 Rnaseq Deseq2 compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tooluniverse Rnaseq Deseq2 this skillwu-yc/LabClaw1.1k2 repos~4.5kAutomated safety check: PassNone
External API ChangeGuyTeichman/RNAlysis139—~1.8kAutomated safety check: PassMIT
Ggetdavila7/claude-code-templates33k10 repos~6.3kAutomated safety check: PassMIT
Ukb Ppp Region FetchClawBio/ClawBio1.2k—~4.6kAutomated safety check: PassMIT
Ggetaipoch/medical-research-skills1.9k—~816Automated safety check: PassMIT
Bio Workflows Scrnaseq PipelineGPTomics/bioSkills1.2k1 repos~5.1kAutomated safety check: PassMIT

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  • Tooluniverse Drug Repurposing

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  • Tooluniverse Expression Data Retrieval

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  • Tooluniverse Gene Enrichment

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Works with

Categories

Questions about Tooluniverse Rnaseq Deseq2

What does Tooluniverse Rnaseq Deseq2 do?

Production-ready RNA-seq differential expression analysis using PyDESeq2. Tooluniverse Rnaseq Deseq2 is an agent skill from wu-yc/LabClaw. Production-ready RNA-seq differential expression analysis using PyDESeq2.

When should I use Tooluniverse Rnaseq Deseq2?

Tooluniverse Rnaseq Deseq2 fits situations like: analyzing RNA-seq count matrices; identifying DEGs; performing differential expression with statistical rigor; answering questions about gene expression changes.

How do I install Tooluniverse Rnaseq Deseq2 in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-rnaseq-deseq2 -a claude-code`. Or copy the skill folder (skills/bio/tooluniverse-rnaseq-deseq2 in wu-yc/LabClaw) into .claude/skills/tooluniverse-rnaseq-deseq2 in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse Rnaseq Deseq2 in Codex?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-rnaseq-deseq2 -a codex`. Or copy the skill folder (skills/bio/tooluniverse-rnaseq-deseq2 in wu-yc/LabClaw) into .agents/skills/tooluniverse-rnaseq-deseq2 in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse Rnaseq Deseq2 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-rnaseq-deseq2 -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-rnaseq-deseq2, .gemini/skills/tooluniverse-rnaseq-deseq2, .github/skills/tooluniverse-rnaseq-deseq2 and .opencode/skills/tooluniverse-rnaseq-deseq2 in your project.

What does Tooluniverse Rnaseq Deseq2 need to run?

Going by SKILL.md and its folder, Tooluniverse Rnaseq Deseq2 needs the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Tooluniverse Rnaseq Deseq2 access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Tooluniverse Rnaseq Deseq2 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 Rnaseq Deseq2 use?

No licence was found for Tooluniverse Rnaseq Deseq2 or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Tooluniverse Rnaseq Deseq2 use?

About 4.5k tokens (SKILL.md is roughly 18k 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 Rnaseq Deseq2?

Skills that share tags, products or a category with Tooluniverse Rnaseq Deseq2: External API Change (GuyTeichman/RNAlysis, 139 stars), Gget (davila7/claude-code-templates, 33k stars), Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars) and Gget (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Rnaseq Deseq2?

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.