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gget

Query 20+ bioinformatics databases via unified CLI and Python interface.

7|Updated Jan 27, 2026
Search Tags:#python#cli#bioinformatics#expression#enrichment#ensembl#gget
One-click install
npx skills add https://github.com/wsxwj123/opencode-skills-backup --skill gget-wsxwj123
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/wsxwj123/opencode-skills-backup/tree/main/gget
Command: npx skills add https://github.com/wsxwj123/opencode-skills-backup --skill gget-wsxwj123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This tool provides fast, unified access to more than twenty bioinformatics databases through a single CLI and Python interface, simplifying discovery and data retrieval across multiple resources.

Core Features & Use Cases

  • Unified CLI and Python interface to query 20+ genomic databases and analyses from a single place.
  • Supports interactive exploration, batch processing, and end-to-end workflows covering gene info, sequences, enrichment, expression, and structural data, and more.
  • Keeps data current with automated checks and biweekly updates; works with modular components like scripts, references, and assets for on-demand tasks.

Quick Start

Install gget in a clean environment and start with a basic search to see results.

Frequently Asked Questions about gget

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query multiple bioinformatics databases using a single Python interface?▼

This tool provides fast, unified access to over twenty bioinformatics databases through a single CLI and Python interface, enabling interactive exploration, batch processing, and end-to-end workflows for genomic data retrieval.

Can I retrieve gene expression and enrichment data from Ensembl via command line?▼

Yes, you can retrieve gene expression and enrichment data from Ensembl via the unified command line interface, which supports quick lookups and automated data integration across multiple genomic resources.

Does the gget tool require pandas to process bioinformatics data?▼

Yes, this tool requires pandas as a dependency to process and integrate bioinformatics data queried from the 20+ supported genomic databases through its Python functions and CLI commands.

What is the best way to integrate structural and sequence data for end-to-end genomic workflows?▼

The best way to integrate structural and sequence data for end-to-end genomic workflows is using a unified interface that supports interactive exploration and batch processing while keeping data current with automated biweekly updates.

Are there limitations when doing batch processing for gene enrichment queries?▼

While batch processing for gene enrichment queries is supported, limitations depend on the external databases; however, automated checks and biweekly updates are implemented to keep the integrated data current and accurate.

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