gget

npx skills add K-Dense-AI/scientific-agent-skills --skill gget --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# 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 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin `gget==0.30.5`; for broken upstream database adapters, update gget after checking release notes. ## Installation Install gget in a clean virtual environment to avoid conflicts: ```bash # Reproducible install targeting this skill uv venv .venv source .venv/bin/activate uv pip install "gget==0.30.5" # In Python/Jupyter import gget ``` ## Quick Start Basic usage pattern for all modules: ```bash # Command-line gget <module> [arguments] [options] # Python gget.module(arguments, options) ``` Most modules return: - **Command-line**: JSON (default) or CSV with `-csv` flag -

Reproducible install targeting this skill
uv venv .venv
source .venv/bin/activate
uv pip install "gget==0.30.5"
In Python/Jupyter
import gget
Command-line
gget <module> [arguments] [options]
Python