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gget

Query genomic databases including Ensembl, UniProt, NCBI via CLI or Python interface.

1|Updated Jan 26, 2026
Search Tags:#CLI#bioinformatics#Python#databases#enrichment#gget#orthology
One-click install
npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gget-victory-hugo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/Victory-Hugo/S2-Agent-Skill/tree/main/skills/genomics/gget
Command: npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gget-victory-hugo

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 CLI and Python interface to query 20+ biological databases, enabling researchers to quickly gather gene information, sequence data, enrichment results, and more without juggling multiple tools.

Core Features & Use Cases

  • Unified access to 20+ genomic resources (Ensembl, UniProt, NCBI, ARCHS4, OpenTargets, etc.) via a single CLI.
  • Dual interface: command-line tools and Python functions for seamless scripting and interactive use.
  • Workflow examples: from gene discovery to enrichment analyses, single-cell data retrieval, and cancer genomics exploration.
  • Use Case: a bioinformatics analyst queries gene candidates, retrieves sequences, expression data, and disease associations to prioritize targets.

Quick Start

  • Install gget with pip: pip install gget
  • Quick example: gget search -s homo_sapiens "BRCA1"
  • Retrieve sequences: gget seq ENSG00000012048

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 like Ensembl and UniProt from the command line?▼

Querying multiple genomic databases via a single CLI interface streamlines bioinformatics research by enabling rapid retrieval of gene information, sequence data, and disease associations without juggling multiple tools. You can use a unified command-line tool to access over 20 resources directly.

Can I retrieve gene sequences and expression data programmatically in Python?▼

Yes, retrieving gene sequences and expression data programmatically in Python is supported through the gget module. This dual interface allows seamless scripting and interactive use for automated, reproducible analyses across databases like NCBI and ARCHS4.

What is the best way to perform gene enrichment analysis and orthology queries across genomic databases?▼

Performing gene enrichment analysis and orthology queries across genomic databases is best handled through a unified Python and CLI interface. This approach applies standard programmatic function calls to gather enrichment results and orthology data efficiently.

Does this bioinformatics tool require specific dependencies to query OpenTargets and ARCHS4?▼

Querying OpenTargets and ARCHS4 requires specific dependencies, specifically the gget package and pandas. These dependencies must be installed via pip to enable standard Python packaging and ensure the CLI commands function correctly for data retrieval.

How do I search for a specific gene like BRCA1 and retrieve its associated disease and drug targets?▼

Searching for a specific gene like BRCA1 and retrieving associated disease and drug targets involves querying OpenTargets via the CLI. You can execute a simple search command for homo_sapiens to discover gene candidates and prioritize targets based on associations.

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