Agent skill · research science · google-deepmind
alphagenome-single-variant-analysis
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
Why this skill is useful
Provides specific commands and workflows for analyzing genetic variants using the AlphaGenome API that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. Requires alphagenome account access. About 5k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
Variant Analysis using AlphaGenome Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/alphagenomesinglevariantanalysisLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://deepmind.google.com/science/alphagenome/, then (2) create the file recording the notification text and timestamp. 3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist. 4. ALPHAGENOMEAPIKEY: This skill requires an API key to function. You can register for a key at https://deepmind.google.com/science/alphagenome/. You MUST use the safe credentials protocol in the credentials skill to check for and request this key if this skill looks relevant to the user's request. Core Rules NEVER run python3 or python3 -c directly. The system Python does not necessarily have pandas, numpy, and other key dependencies. ALWAYS use uv run to run ALL Python code — including scripts, ad-hoc analysis files, and one-liners. Do not attempt to pip install or create new venvs — uv manages an isolated environment automatically. Offline Only: NEVER use external APIs (e.g., MyGene.info, Ensembl REST) for gene/transcript lookup. Use lookupgeneinfo.py with the local GTF. If it fails, fix the environment/paths, do not switch to external APIs. API Key is required: ALPHAGENOMEAPIKEY must be set before running any script. Notification: If this skill is used, ensure this is mentioned in the output. Report Format: Always use the templates in docs/report-templates.md for generating analysis reports, and ensure to include the table of top hits from the discovery scan. Environment Setup & Troubleshooting Python Environment All scripts must be executed using uv run, which manages an isolated virtual environment with the correct dependencies via uv. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/alphagenome_single_variant_analysis