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gget

Query genomic data across 20+ databases via CLI and Python API.

6|Updated Dec 30, 2025
Search Tags:#bioinformatics#expression#sequence#enrichment#multidatabase#gene-information
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill gget-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/gget
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill gget-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

gget provides a unified interface to query and fetch data from 20+ genomic databases, simplifying discovery across multiple resources.

Core Features & Use Cases

  • Unified CLI and Python interface to access 20+ genomic resources.
  • Cross-database queries for gene info, sequences, expression, and disease associations.
  • Real-world workflow example: quickly compile gene info and associated tissues and enrichment for a list of candidate genes.

Quick Start

Query a gene like ACE2 to retrieve metadata, sequences, tissue expression, and enrichment results in seconds.

Frequently Asked Questions about gget

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

FAQPage Schema
How do I query gene information and sequences across multiple genomic databases at once?▼

Unified bioinformatics queries across databases are achieved by fetching data from 20+ resources like Ensembl, UniProt, and NCBI to accelerate gene discovery and analysis through a CLI and Python API.

What's the best way to retrieve tissue expression profiles and pathway enrichment results for a list of candidate genes?▼

Retrieving tissue expression profiles and pathway enrichment results for candidate genes is handled by querying ARCHS4 and OpenTargets, compiling associated tissues and enrichment data in seconds for human and model organisms.

Can I integrate genomic data from Ensembl and UniProt into a single reproducible workflow?▼

Integrating genomic data from Ensembl and UniProt into a reproducible workflow is supported, fetching sequences and metadata while handling network errors to ensure consistent outputs.

Does gget support bioinformatics queries for both human and model organisms?▼

Yes, bioinformatics queries for both human and model organisms are supported, allowing you to retrieve gene metadata, expression data, and disease associations across multiple species.

How do I compile gene metadata and disease associations without manually searching separate databases?▼

Compiling gene metadata and disease associations without manual searches is done by cross-referencing 20+ genomic databases through a single interface, eliminating the need to query OpenTargets or NCBI individually.

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