alphagenome

library0.6.1pypypi✓ verified 80d ago

A Python SDK developed by Google DeepMind for interacting with and visualizing genomic models. Currently at version 0.6.1, it supports interval scoring, in-silico mutagenesis, variant normalization, and sequence logo plotting. Requires Python >=3.10 and has a rapid release cadence (minor versions every few weeks).

ai-ml gcp

pip install alphagenome

github ↗package ↗docs ↗

INSTALL

IMPORT

SIG · ALPHAGENOME

alphagenome

ai-mlpythonv0.6.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

AlphaGenome

✓ import alphagenome

✗ from alphagenome import AlphaGenome

Initialize a model, predict tracks for a genomic interval.

from alphagenome import AlphaGenome, Interval, GRCh38 import os # Initialize the model (requires API key via environment variable) api_key = os.environ.get("ALPHAGENOME_API_KEY", "") model = AlphaGenome(api_key=api_key) # Define an interval and get predictions interval = Interval(chrom="chr1", start=10000, end=20000) tracks = model.predict_sequence(interval, genome=GRCh38) print(tracks)

Debug

Known issues

breakingIn v0.5.0, support for 2kb DNA sequence lengths was removed. AlphaGenome performs poorly with very short sequences, so any code relying on intervals < ~10kb may break or produce unreliable results.

fix

Use intervals >= 10kb or set a larger width. Remove any hardcoded 2kb assumptions.

affects: >=0.5.0

deprecatedIn v0.6.0, `filter_by_strand` on Output dataclass now correctly filters splice junctions. Previously only tracks were filtered; if your code depended on the old behavior (unfiltered junctions), update filtering logic.

fix

After upgrading to v0.6.0, verify that filtering by strand works as expected for both tracks and junctions.

affects: <0.6.0

gotchaThe API key must be set via environment variable `ALPHAGENOME_API_KEY` or passed directly; otherwise calls will fail with authentication errors. The SDK does not prompt for a key.

fix

Set the environment variable before using AlphaGenome: os.environ['ALPHAGENOME_API_KEY'] = 'your_key'

affects: all

Upgrade

Version history

0.6.1latest on PyPI · released Mar 3, 2026

Audit

Dependencies

numpyrequiredCore dependency for array operations

matplotlibrequiredRequired for plotting (seqlogo, tracks)

pandasrequiredUsed for data handling and anndata tidying

anndataoptionalRequired only for tidy_anndata functionality

Agent activity

66 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/google-deepmind/alphagenome ↗

packagehttps://pypi.org/project/alphagenome/ ↗

docshttps://www.alphagenomedocs.com/ ↗