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alterlab-reactome

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Programmatically explore Reactome pathways.

Education & Research#python#bioinformatics#enrichment#rest-api#reactome#pathway-analysis
AuthorAlterLab-IEU
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Query and analyze Reactome data programmatically by accessing the ContentService and AnalysisService REST APIs.

Core Features & Use Cases

  • Content & Entity Queries: Retrieve pathway information, participating entities, and pathway definitions using REST endpoints.
  • Pathway Analysis & Visualization: Perform overrepresentation and expression analyses, manage analysis tokens, and view results in the Pathway Browser.
  • CLI + Library Support: Use the Python CLI (scripts/reactome_query.py) to automate common tasks and integrate with pipelines.

Quick Start

Use the Reactome CLI (scripts/reactome_query.py) to query a pathway by ID or perform enrichment analysis on a gene list.

Dependency Matrix

Required Modules

requests

Components

scriptsreferences

💻 Claude Code Installation

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Please help me install this Skill:
Name: alterlab-reactome
Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-reactome

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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