RaMP – Relational database of Metabolomics Pathways

RaMP integrates gene and metabolite biological pathway information from multiple sources, including KEGG, HMDB, Reactome, and WikiPathways.  RaMP is integrated into an R package, including an R shiny web app that performs basic queries and pathway enrichment analysis.

For access, please access on our GitHub repository.  Access publication here.

IntLIM – Integration of omics data through LInear Modeling

Our goal for developing IntLIM is to provide a user-friendly approach to integrating metabolomics and transcriptomic data acquired in large sample sets (e.g. epidemiological studies).  For integration, we propose a linear modeling approach that describes how gene-metabolite associations are affected by phenotype.

For more information and to access the code, please click here. Access preprint here.

ALTRE – defines ALTered Regulatory Elements from chromatin accessibility data.

The software provides a workflow in the form of an R package and an associated R Shiny app for the comparison of regulatory elements (e.g. candidate promoters and enhancers) between two different cell types.

To access the latest release with instructions and an example dataset, click here.

COMETS Analytics – Metabolomics analysis for epidemiological studies.

Metabolomics analysis tool that supports harmonization of metabolites and correlation analysis, and includes customizable visualization. Click here for access.