# Alphagenome Single Variant Analysis

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Design
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill alphagenome-single-variant-analysis -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill alphagenome-single-variant-analysis -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill alphagenome-single-variant-analysis -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill alphagenome-single-variant-analysis -g -a gemini-cli -y`

## Description

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Variant Analysis using AlphaGenome

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If
    .licenses/alphagenome_single_variant_analysis_LICENSE.txt does not already
    exist in the workspace root directory then (1) prominently notify the user
    to check the terms at https://deepmind.google.com/science/alphagenome/, then
    (2) create the file recording the notification text and timestamp.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`ALPHAGENOME_API_KEY`**: This skill requires an API key to function.

    You can register for a key at https://deepmind.google.com/science/alphagenome/.
    You **MUST** use the safe credentials protocol in the `credentials` skill to
    check for and request this key if this skill looks relevant to the user's request.
5.  **`ALPHAGENOME_GTF_PATH` (Optional)**: Accelerate gene/transcript lookup by
    pointing to a local copy of the GTF feather file instead of downloading from
    GCS:

    ```bash
    echo "ALPHAGENOME_GTF_PATH=/path/to/local/gencode.v46.annotation.gtf.gz.feather" >> ~/.env
    ```

## Core Rules

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/alphagenome_single_variant_analysis/SKILL.md