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数据与研究

gget

k-dense-ai/scie…t-skills

Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill gget

SKILL.md

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"

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