# Alphagenome Atlas Website Links

Constructs deep-links and URLs for the AlphaGenome Atlas website.

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- 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-atlas-website-links -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill alphagenome-atlas-website-links -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill alphagenome-atlas-website-links -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill alphagenome-atlas-website-links -g -a gemini-cli -y`

## Description

Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based VCF-style coordinates), genomic locus views (1-based closed chr:start-end), candidate summary tables, and AlphaGenome reference vs. alternate predictions. Use when visualizing, exploring, charting, or linking genetic variants and genomic loci on the AlphaGenome Atlas, or when asked to inspect, view, or link predictions for a genomic variant. Don't use for computing raw AlphaGenome variant predictions directly without Atlas URLs (use alphagenome-single-variant-analysis or alphagenome-variant-impact-score).

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

# AlphaGenome Atlas Deep-Linking & URL Configuration

Construct and validate deep-links for the AlphaGenome Atlas web application
(`https://deepmind.google.com/science/alphagenome/atlas`).

Base URL: `https://deepmind.google.com/science/alphagenome/atlas`

> [!IMPORTANT] **Mandatory Atlas Deep-Linking with Variant Scores**: Whenever
> presenting, discussing, or scoring genetic variants, you **MUST always provide
> clickable deep-links to the
> [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**.
> Use `scripts/alphagenome_atlas_links.py` to automate link and table
> generation.

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## Prerequisites

```bash
# 1. Single Variant Exploration Link:
uv run scripts/alphagenome_atlas_links.py variant "chr9:128225994:G>A" \
  --biosample K562 \
  --modalities RNA_SEQ,DNASE,CHIP_TF

# 2. Genomic Locus / Interval Link:
uv run scripts/alphagenome_atlas_links.py locus "chr11:5288500-5290500" \
  --biosample K562 \
  --modalities RNA_SEQ,DNASE,CHIP_TF

# 3. Format Candidate Variant Records Table (with embedded clickable links):
uv run scripts/alphagenome_atlas_links.py table --input top_variants.json --biosample K562

# 4. Construct Ref vs. Alt Track Predictions Link (/atlas/track-predictions):
uv run scripts/alphagenome_atlas_links.py track-predictions \
  --variant "chr15:42387805:C>G" \
  --gene CAPN3 \
  --biosample "Muscle_Skeletal"
```

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## 2. URL Query Parameters

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