RaMP

RaMP (Relational database of Metabolomics Pathways) is a software tool that facilitates the integrated analysis and interpretation of metabolomics data with other omics data, particularly transcriptomics, at the pathway level. It combines biological pathways from various databases, including KEGG, Reactome, WikiPathways, and HMDB, to provide a comprehensive resource for mapping genes and metabolites to biochemical and disease pathways.

Key features of RaMP include:

1. Batch and complex queries: Users can perform queries listing all metabolites involved in a specific pathway or disease.

2. Integration with pathway analysis tools: RaMP can easily be integrated into existing software.

3. Pathway overrepresentation analysis: Given a list of genes or metabolites of interest, RaMP supports pathway overrepresentation analysis.

4. User-friendly interface: The RaMP R package includes an RShiny web application that supports simple and batch queries, pathway overrepresentation analysis, and network visualization of gene-metabolite relationships.

5. Stand-alone framework: The package includes a raw database file (MySQL dump) and Python code to recreate the database. It is a stand-alone, downloadable framework for public use and integration with other tools.