Overview
alphagenome is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “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-histo…”. The project has 46k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/alphagenome`.
What alphagenome does
AlphaGenome is DeepMind's sequence-to-function model: 1 Mb of DNA in, base-pair predictions for eleven assay types across thousands of human and mouse tracks out. The **AlphaGenome Atlas** (released 2026-09-08) is that model run once over every possible single-nucleotide change in GRCh38, about 9 billion variants, stored with a single ranking number, the **AlphaGenome Variant Impact (AVI)** score, its genome-wide percentile, and an 18-way attribution of what drives it. Both are reached through one `pip install alphagenome` and one API key.
What’s inside
The SKILL.md for alphagenome is organised into these sections:
- When to use which
- Setup
- The coordinate contract
- Atlas workflow
- 1. Rank with AVI
- 2. Resolve the mechanism by track
- 3. Send the reader to the portal
- In Python
- Model workflow
- Score variants the Atlas does not hold
- Predict tracks and mutagenise
- Reading the numbers
Installation
Add alphagenome to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/alphagenomeReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
alphagenome is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 45,887 GitHub stars
- Actively maintained — repository updated in the last 30 days
- Its repository gained 1,026 GitHub stars over the last 7 days
Author
Topics
Frequently asked questions
- What does alphagenome do?
- 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 user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.
- How do I install alphagenome?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/alphagenome in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is alphagenome free to use?
- Yes. alphagenome is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does alphagenome come from?
- alphagenome ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 45,887 GitHub stars apply to that whole collection, not to this skill on its own.