Agent skill

Gtex Database

by google-deepmind in google-deepmind/science-skills

A skill your agent uses when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

Apache-2.0Auto-check passedResearch & Science

Install Gtex Database

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a claude-code

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

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database --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/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gtex_database .claude/skills/gtex-database && 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/

Paste into Claude Code

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .claude/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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

$skill-installer install https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database

Type 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.

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gtex_database .agents/skills/gtex-database && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .agents/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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.

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gtex_database .cursor/skills/gtex-database && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .cursor/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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

$ gemini skills install https://github.com/google-deepmind/science-skills.git --path skills/gtex_database

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gtex_database .gemini/skills/gtex-database && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .gemini/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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.

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database

Installs 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).

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gtex_database .github/skills/gtex-database && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .github/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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.

skills CLI

$ npx skills add google-deepmind/science-skills --skill gtex-database -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills gtex-database --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gtex_database .opencode/skills/gtex-database && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "gtex-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gtex_database into .opencode/skills/gtex-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gtex-database", 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: gtex-database
GitHub stars: 3.2k
Used in: 3 other repos
Token cost: ~1.5k tokens
SKILL.md length: 607 words
Files: 3 (incl. scripts, references)
Skills in repo: 40
Repo updated: Sep 15, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

A skill your agent uses when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

Works in 5 steps: resolve-gencode-id — Gene Symbol →… → get-median-expression — Get Median… → get-top-expressed-tissues — Get Top… → …
Research & Science work in your project
SKILL.md covers Prerequisites, When to Use, Core Rules and Command Selection Guide, plus 3 more sections
Runs Python scripts from its folder; calls uv

What it does

Gtex Database is an agent skill from google-deepmind/science-skills. Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts and reference files (for example `scripts/gtex_cli.py`).

It sits in Research & Science. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.

When your agent uses it

Research & Science work in your project

Example prompts

“/gtex-database”

Requirements

Python 3

Workflow steps

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

resolve-gencode-id — Gene Symbol → GENCODE ID
get-median-expression — Get Median Expression (TPM)
get-top-expressed-tissues — Get Top Expressed Tissues
get-gene-eqtls — Get All eQTLs for a Gene
get-eqtls-in-region — Get eQTLs in Chromosomal Region

What it can do on your machine

Read from SKILL.md and the folder at commit 6883275. 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
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- uv
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):
- gtexportal.org
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

Gtex Database loads about 1.5k tokens when it runs, and up to ~3k if it reads all its reference files. Until then it costs about 48 tokens; SKILL.md has 607 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~48
When it runs · the whole SKILL.md, loaded when a task matches: ~1.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~3k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 607 words, ~1,515 tokens.

Download SKILL.mdSave it as .claude/skills/gtex-database/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: gtex-database
description: Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

GTEx Database Integration

This skill retrieves transcriptomics data (RNA expression baselines) and expression Quantitative Trait Loci (eQTLs) from the GTEx Portal API V2. It provides access to median TPM (Transcripts Per Million) values for genes and significant eQTLs for variants across 54 human tissue sites.

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If .licenses/gtex_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://gtexportal.org/home/license and https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the file recording the notification text and timestamp.

When to Use

Use this skill when you need to:

Map a gene symbol to its Versioned GENCODE ID.
Retrieve the baseline median expression level (in TPM) of a gene across various tissues.
Find the top tissues where a particular gene is most highly expressed.
Fetch significant single-tissue eQTLs for a variant or within a chromosomal window.
Get all significant eQTLs associated with a specific gene.
Contextualise a variant within GWAS loci using eQTL data.

Do NOT use when you need to:

Query for protein-level expression or post-translational modifications (PTMs). GTEx only measures mRNA abundance.
Query gene expression in diseased tissues (e.g., tumor samples, cirrhosis). GTEx is a baseline atlas of normal, non-diseased tissues.
Query embryonic or fetal gene expression. GTEx donors are adults only.

Core Rules

CRITICAL: You MUST respect GTEx Portal API Terms of Use.

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
Limit requests to maximum 250 items per page where applicable.
Notification: If this skill is used, ensure this is mentioned in the output.

Command Selection Guide

Pick the right command on the first try. Match the user's input to the correct subcommand below.

Map a gene symbol to GENCODE ID: resolve-gencode-id
Get median expression (TPM) for a gene: get-median-expression
Find tissues with highest expression for a gene: get-top-expressed-tissues
Get all eQTLs for a specific gene: get-gene-eqtls
Find eQTLs within a chromosomal region: get-eqtls-in-region

Show full SKILL.md (255 more words)Show less

Quick Start

bash

# Map the TNF gene symbol to its GENCODE ID
uv run scripts/gtex_cli.py resolve-gencode-id TNF --output /tmp/tnf_id.json

# Get median expression of a gene by GENCODE ID
uv run scripts/gtex_cli.py get-median-expression ENSG00000232810.2 --output /tmp/tnf_expr.json

All subcommands write JSON to disk. Always save output in the /tmp/ directory. The default output file is /tmp/gtex_output.json if --output is not specified.

Commands

1. `resolve-gencode-id` — Gene Symbol → GENCODE ID

Maps a standard gene symbol (e.g., "JUN", "TNF") to its Versioned GENCODE ID. This ID is required for all other expression and eQTL calls.

bash

uv run scripts/gtex_cli.py resolve-gencode-id TNF --output /tmp/tnf_id.json

Arguments:

gene_symbol (positional): The standard gene symbol (e.g., "TNF").
--output: Output file path (default: /tmp/gtex_output.json).

2. `get-median-expression` — Get Median Expression (TPM)

Retrieves the median TPM for a gene across all 54 GTEx tissue sites or specified tissues.

bash

uv run scripts/gtex_cli.py get-median-expression ENSG00000232810.2 \
  --tissues "Whole Blood,Spleen" --output /tmp/expr.json

Arguments:

gencode_id (positional): The Versioned GENCODE ID.
--tissues: Comma-separated list of tissue IDs (optional, defaults to all 54 tissues).
--output: Output file path (default: /tmp/gtex_output.json).

3. `get-top-expressed-tissues` — Get Top Expressed Tissues

Returns the n tissues with the highest median expression for the target gene.

bash

uv run scripts/gtex_cli.py get-top-expressed-tissues ENSG00000232810.2 \
  --n 5 --output /tmp/top_tissues.json

Arguments:

gencode_id (positional): The Versioned GENCODE ID.
--n: Number of top tissues to return (default: 5).
--output: Output file path.

4. `get-gene-eqtls` — Get All eQTLs for a Gene

Returns every significant eQTL associated with the gene across specified tissues.

bash

uv run scripts/gtex_cli.py get-gene-eqtls ENSG00000232810.2 \
  --tissues "Whole Blood" --output /tmp/eqtls.json

Arguments:

gencode_id (positional): The Versioned GENCODE ID.
--tissues: Comma-separated list of tissue IDs (optional, defaults to all).
--output: Output file path.

5. `get-eqtls-in-region` — Get eQTLs in Chromosomal Region

Returns all significant single-tissue eQTLs within a chromosomal window (up to 8Mb).

bash

uv run scripts/gtex_cli.py get-eqtls-in-region chr17 7000000 7100000 "Esophagus - Muscularis" \
  --output /tmp/region_eqtls.json

Arguments:

chromosome (positional): Chromosome name (e.g., chr17).
start (positional): Start position.
end (positional): End position (max 8Mb from start).
tissue_id (positional): The target tissue ID.
--output: Output file path.

Typical Workflows

Identify highest expressing tissues for a gene

bash

# Step 1: Map symbol to GENCODE ID
uv run scripts/gtex_cli.py resolve-gencode-id GATA4 --output /tmp/gata4_id.json

# Step 2: Query for top tissues using the resolved ID
uv run scripts/gtex_cli.py get-top-expressed-tissues <gencode_id> --n 5 \
  --output /tmp/gata4_top.json

Files

SKILL.md and 2 other files (scripts, references) in skills/gtex_database of google-deepmind/science-skills.

SKILL.md
references/citation.bib
scripts/gtex_cli.py

Open the folder on GitHubat commit 6883275

Used in 3 other repositories

We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Gtex Database 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.

Gtex Database compared with similar skills
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Nature Paper CardYuan1z0825/nature-skills	46k	2 repos	~2.1k	Automated safety check: Pass	Apache-2.0	yesterday
Read arXiv Paperkarpathy/nanochat	58k	2 repos	~494	Automated safety check: Pass	MIT	1 mo ago
Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today

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Questions about Gtex Database

What does Gtex Database do?

A skill your agent uses when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites. Gtex Database is an agent skill from google-deepmind/science-skills. Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

When should I use Gtex Database?

Gtex Database fits situations like: research & Science work in your project.

How do I install Gtex Database in Claude Code?

Run `npx skills add google-deepmind/science-skills --skill gtex-database -a claude-code`. Or copy the skill folder (skills/gtex_database in google-deepmind/science-skills) into .claude/skills/gtex-database in your project. Claude Code loads it when a task matches its description.

How do I install Gtex Database in Codex?

Run `npx skills add google-deepmind/science-skills --skill gtex-database -a codex`. Or copy the skill folder (skills/gtex_database in google-deepmind/science-skills) into .agents/skills/gtex-database in your project. Codex loads it when a task matches its description.

Can I use Gtex Database 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 google-deepmind/science-skills --skill gtex-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gtex-database, .gemini/skills/gtex-database, .github/skills/gtex-database and .opencode/skills/gtex-database in your project.

What does Gtex Database need to run?

Going by SKILL.md and its folder, Gtex Database needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.

Does Gtex Database access the network?

SKILL.md names 1 domain. As links in the text: gtexportal.org. This is read from the text; nothing was executed.

Is Gtex Database 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Gtex Database use?

Gtex Database is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gtex Database use?

About 1.5k tokens (SKILL.md is roughly 6.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.5k tokens, read only when the agent opens those files.

What are the alternatives to Gtex Database?

Skills that share tags, products or a category with Gtex Database: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gtex Database?

google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,220 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on September 15, 2026.

Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Gtex Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

GTEx Database Integration

Prerequisites

When to Use

Core Rules

Command Selection Guide

Quick Start

Commands

1. resolve-gencode-id — Gene Symbol → GENCODE ID

2. get-median-expression — Get Median Expression (TPM)

3. get-top-expressed-tissues — Get Top Expressed Tissues

4. get-gene-eqtls — Get All eQTLs for a Gene

5. get-eqtls-in-region — Get eQTLs in Chromosomal Region

Typical Workflows

Identify highest expressing tissues for a gene

Files

Used in 3 other repositories

Compare with similar skills

Similar skills

More from google-deepmind/science-skills

Related

Questions about Gtex Database

1. `resolve-gencode-id` — Gene Symbol → GENCODE ID

2. `get-median-expression` — Get Median Expression (TPM)

3. `get-top-expressed-tissues` — Get Top Expressed Tissues

4. `get-gene-eqtls` — Get All eQTLs for a Gene

5. `get-eqtls-in-region` — Get eQTLs in Chromosomal Region