Menu

Individual skill

alphagenome

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.

plugins/KalarisLabs/research-agent-skills/skills/alphagenome/SKILL.md

Read pinned source

Source commit d780783eba4ecc7c8b9429f95c9362df95f07c61

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
Yes
Repository scan complete
No
Skill scan complete
No
Observed behavior
Network or broad shell
Last checked
Nov 4, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
1,530
Repository last updated
Nov 6, 2026
License
Apache-2.0

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Declared tags are partial or unavailable.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt

# AlphaGenome and the AlphaGenome Atlas

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.

> Research and theoretical modelling only. Outputs must not be used to train
> other models, and are not for diagnostic procedures or medical decisions.

## When to use which