alphagenome

80 / 100 · Low risk

Fine to try.

By KalarisLabs/research-agent-skills (GitHub) · research · 126 stars · scanned at commit 802bbea

Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and build Atlas website deep links. Use when the …

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this.

Found in 4 places.

skills/alphagenome/SKILL.md, line 30Both are reached through one `pip install alphagenome` and one API key.
skills/alphagenome/SKILL.md, line 49uv pip install alphagenome # PyPI; tested on Python 3.12 and 3.13, alphagenome 0.9.0
skills/alphagenome/references/model-api.md, line 9uv pip install alphagenome # PyPI; Python >= 3.10, tested here on 3.12 and 3.13

Show 1 more

skills/alphagenome/scripts/_common.py, line 100"alphagenome is not installed. Run: uv pip install alphagenome "

Runs commands on your computer

The author does not mention this.

Found in 5 places.

skills/alphagenome/SKILL.md, line 49uv pip install alphagenome # PyPI; tested on Python 3.12 and 3.13, alphagenome 0.9.0
skills/alphagenome/SKILL.md, line 77python atlas_query.py avi --variant chr22:36201698:A>C chr9:128225994:G>A
skills/alphagenome/SKILL.md, line 110python atlas_query.py scorers # what the server serves right now

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skills/alphagenome/SKILL.md, line 129python atlas_link.py variant chr22:36201698:A>C --biosample "colon" --modalities RNA_SEQ,DNASE,CHIP_TF
skills/alphagenome/SKILL.md, line 167python score_variants.py --variant chr22:36201698:A>C -o scores.tsv # 12 recommended scorers, 1 Mb

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'alphagenome' ] || [ -L ~/.agents/skills/'alphagenome' ]; then echo 'A skill folder named alphagenome already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/KalarisLabs/research-agent-skills' "$d" && git -C "$d" checkout --quiet '802bbea44e551abac24d6856f83fc55149bbdba3' -- 'skills/alphagenome' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/alphagenome' ~/.agents/skills/'alphagenome' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'alphagenome' ~/.claude/skills/'alphagenome' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-13	`802bbea`	80
2026-11-07	`29fe36d`	80