Alphagenome Atlas Website Links
Constructs deep-links and URLs for the AlphaGenome Atlas website.
Install
npx skills add google-deepmind/science-skills --skill alphagenome-atlas-website-links -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Engineering
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,960 tokens
- Runs scripts
- Yes, review before use
What it does
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).
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. Use
scripts/alphagenome_atlas_links.pyto automate link and table generation.
Prerequisites
# 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"
