What biological entities can I query with this skill?

You can query human pathways, reactions, proteins, small molecules, drugs, and molecular complexes, with support for identifiers like UniProt, Ensembl, ChEBI, and EntrezGene IDs.

Does this skill support quantitative expression data?

Yes, it supports expression data analysis using TSV formats, allowing Claude to process numeric values from samples and identify relevant biological pathways.

How do I visualize the results of a pathway analysis?

The skill utilizes analysis tokens that persist for 7 days. Claude can generate specific URLs that open your analysis results directly in the Reactome Pathway Browser.

Can I perform analysis on species other than humans?

Yes, the skill supports species projection, which allows you to map identifiers from other organisms onto the well-annotated human pathway framework for comparative studies.

Reactome Pathway Analysis

Name: Reactome Pathway Analysis
Author: BbgnsurfTech

byBbgnsurfTech

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Data Science & ML

Facilitates biological pathway analysis and gene-mapping by querying the Reactome open-source database and REST API.

The Reactome Database skill empowers Claude to perform complex systems biology tasks by interfacing with a curated collection of over 2,800 human biological pathways. It provides specialized capabilities for pathway enrichment analysis, gene expression mapping, and molecular interaction queries via the Reactome REST API and Python clients. This skill is an essential tool for bioinformaticians and researchers who need to identify statistically significant pathways from gene lists, explore disease-related mechanisms, or visualize molecular reactions directly within their automated research workflows.

Key Features

01Quantitative gene expression data analysis and mapping

02Overrepresentation analysis for gene and protein lists

03Cross-species pathway projection and comparative analysis

043 GitHub stars

05Direct integration with Reactome Content and Analysis REST services

06Detailed retrieval of biological pathways, reactions, and complexes

Use Cases

01Identifying metabolic pathways enriched in a list of differentially expressed genes

02Visualizing comparative pathway data across different species for evolutionary biology research

03Mapping protein-protein interactions within specific cellular compartments for drug discovery

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection reactome-database

For use in Claude.ai and ChatGPT

Download Skill