Can I visualize the analysis results graphically?

The skill provides the ability to generate specific URLs that open your analysis results directly in the interactive Reactome Pathway Browser.

How long do the analysis results remain available?

Analysis results are associated with a token that remains valid on the Reactome servers for 7 days, allowing for persistent retrieval and visualization.

Which biological identifiers are supported by this skill?

The skill supports a wide range of identifiers including UniProt accessions, Gene symbols (HGNC), Ensembl IDs, EntrezGene IDs, and ChEBI IDs for small molecules.

Can I perform statistical analysis on gene expression data?

Yes, the skill can process TSV expression datasets to identify relevant biological pathways based on quantitative values and generate statistical metrics like p-values and FDR.

Does this skill require any local database installation?

No, it interacts directly with the Reactome Content and Analysis REST API services, ensuring you always have access to the latest curated pathway data.

Reactome Pathway Analysis

Name: Reactome Pathway Analysis
Author: pur3v4d3r

bypur3v4d3r

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データサイエンスとML

Interfaces with the Reactome REST API to perform biological pathway analysis, gene enrichment, and molecular interaction mapping for systems biology research.

概要

This skill empowers researchers and bioinformatics developers to seamlessly integrate Reactome's curated biological pathway database into their AI-driven workflows. It provides specialized tools for performing overrepresentation and expression analysis, mapping gene or protein identifiers to human pathways, and exploring complex molecular interactions. By providing automated access to the Reactome Content and Analysis services, the skill enables users to analyze high-throughput data, investigate disease mechanisms, and generate direct visualization links for the Reactome Pathway Browser without leaving the development environment.

主な機能

Direct retrieval of pathway hierarchies, reactions, and molecular interactions
Visualization link generation for interactive analysis in the Reactome Browser
1 GitHub stars
Overrepresentation and statistical enrichment analysis for gene/protein lists
Automated identifier mapping for UniProt, Ensembl, Entrez, and ChEBI
Quantitative expression data analysis with support for multi-sample datasets

ユースケース

Mapping diverse biological identifiers to curated human pathway hierarchies
Identifying statistically significant biological pathways from differential expression results
Investigating molecular mechanisms and participating entities within specific disease pathways

概要

主な機能

Direct retrieval of pathway hierarchies, reactions, and molecular interactions
Visualization link generation for interactive analysis in the Reactome Browser
1 GitHub stars
Overrepresentation and statistical enrichment analysis for gene/protein lists
Automated identifier mapping for UniProt, Ensembl, Entrez, and ChEBI
Quantitative expression data analysis with support for multi-sample datasets

ユースケース

Mapping diverse biological identifiers to curated human pathway hierarchies
Identifying statistically significant biological pathways from differential expression results
Investigating molecular mechanisms and participating entities within specific disease pathways