Alphagenome Single Variant Analysis
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility...
Install
npx skills add google-deepmind/science-skills --skill alphagenome-single-variant-analysis -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Design
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,832 tokens
- Runs scripts
- Yes, review before use
What it does
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.
Variant Analysis using AlphaGenome
Prerequisites
-
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH. -
User Notification: If .licenses/alphagenome_single_variant_analysis_LICENSE.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.
-
.envfile: Make sure the.envfile exists in your home directory. Create one if it does not exist. -
ALPHAGENOME_API_KEY: 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
credentialsskill to check for and request this key if this skill looks relevant to the user's request. -
ALPHAGENOME_GTF_PATH(Optional): Accelerate gene/transcript lookup by pointing to a local copy of the GTF feather file instead of downloading from GCS:echo "ALPHAGENOME_GTF_PATH=/path/to/local/gencode.v46.annotation.gtf.gz.feather" >> ~/.env
