gget

Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions.

Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.8 (reviewed 2026-09-30). For reproducible work, pin gget==0.30.8; for broken upstream database adapters, update gget after checking release notes.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Reproducible install targeting this skill
uv venv --python 3.13 .venv
source .venv/bin/activate
uv pip install "gget==0.30.8"