Skills for Real Engineers. Straight from my .agents directory.
39 skills
alphagenome-atlas-website-links
Agent skill from
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).
How to install alphagenome-atlas-website-links
install alphagenome-atlas-website-links
# install the science-skills pack with the skills CLI
npx skills add google-deepmind/science-skills# or add only this skill to Claude Code: copy the folder
skills/alphagenome_atlas_website_links/
# into
~/.claude/skills/alphagenome_atlas_website_links/ (all projects)
.claude/skills/alphagenome_atlas_website_links/ (one project)
1# AlphaGenome Atlas Deep-Linking & URL Configuration23Construct and validate deep-links for the AlphaGenome Atlas web application4(`https://deepmind.google.com/science/alphagenome/atlas`).56Base URL: `https://deepmind.google.com/science/alphagenome/atlas`78> [!IMPORTANT] **Mandatory Atlas Deep-Linking with Variant Scores**: Whenever9> presenting, discussing, or scoring genetic variants, you **MUST always provide10> clickable deep-links to the11> [AlphaGenome Atlas](https://deepmind.google.com/science/alphagenome/atlas)**.12> Use `scripts/alphagenome_atlas_links.py` to automate link and table13> generation.1415--------------------------------------------------------------------------------1617## Prerequisites1819```bash20# 1. Single Variant Exploration Link:21uv run scripts/alphagenome_atlas_links.py variant "chr9:128225994:G>A" \22 --biosample K562 \23 --modalities RNA_SEQ,DNASE,CHIP_TF2425# 2. Genomic Locus / Interval Link:26uv run scripts/alphagenome_atlas_links.py locus "chr11:5288500-5290500" \27 --biosample K562 \28 --modalities RNA_SEQ,DNASE,CHIP_TF2930# 3. Format Candidate Variant Records Table (with embedded clickable links):31uv run scripts/alphagenome_atlas_links.py table --input top_variants.json --biosample K5623233# 4. Construct Ref vs. Alt Track Predictions Link (/atlas/track-predictions):34uv run scripts/alphagenome_atlas_links.py track-predictions \35 --variant "chr15:42387805:C>G" \36 --gene CAPN3 \37 --biosample "Muscle_Skeletal"38```39…
Excerpt shown under the repository's Apache-2.0 license.
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