reactome-skill
Installation
SKILL.md
When to Use
- You have a list of genes/proteins and want to run pathway overrepresentation (enrichment) analysis against Reactome.
- You need to retrieve curated pathway content (hierarchy, reactions, participants) by Reactome stable IDs (e.g.,
R-HSA-69278). - You want to map expression values onto pathways to support pathway-level interpretation.
- You need to project pathways across species/organisms using Reactome’s species projection capabilities.
- You are building a systems biology workflow that requires programmatic access to Reactome via its REST API.
Key Features
- Pathway enrichment (overrepresentation) for identifier lists.
- Expression analysis by mapping expression data to Reactome pathways.
- Content retrieval for pathways, reactions, and participating molecules.
- Pathway hierarchy access to navigate curated pathway structures.
- Species projection to map pathways across organisms.
- API documentation reference: see
references/api_reference.md.