Can I visualize the analysis results?

The skill helps generate specific URLs containing analysis tokens that allow you to visualize your results directly in the Reactome Pathway Browser.

Does this skill support gene expression data?

Yes, it provides tools to submit TSV formatted expression data for quantitative pathway analysis and identifies relevant biological pathways based on expression values.

Which biological identifiers are supported?

Reactome supports a wide range of identifiers including UniProt accessions, Gene Symbols, Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

What is the Reactome Database skill used for?

It is used to query curated biological pathway data, perform enrichment analysis on gene or protein lists, and explore molecular interactions via the Reactome REST API.

Reactome Database

Name: Reactome Database
Author: x-cmd

byx-cmd

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Data Science & ML

Queries the Reactome REST API for pathway analysis, gene enrichment, and molecular interaction mapping in systems biology studies.

This skill empowers researchers and developers to integrate Reactome's peer-reviewed pathway database directly into AI-driven workflows. It provides specialized support for performing overrepresentation analysis, mapping gene lists to biological processes, and retrieving detailed information on molecular reactions and complexes. By leveraging both the Content and Analysis REST APIs, it simplifies complex bioinformatics tasks like species projection and expression data visualization, making it an essential tool for computational biology, drug discovery, and genomic research.

Key Features

018 GitHub stars

02Pathway enrichment and overrepresentation analysis

03Support for expression data and species projection

04Automated result visualization in Reactome Pathway Browser

05Gene and protein mapping to biological pathways

06REST API integration for Content and Analysis services

Use Cases

01Analyzing large-scale gene expression datasets for pathway relevance

02Programmatically querying molecular interactions and entity hierarchies

03Identifying statistically significant biological pathways from gene lists

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill reactome-database

For use in Claude.ai and ChatGPT

Download Skill