Metabolomics resources in the Saez Lab

Last updated: 5 October 2024

In the Saez Lab over the recent years, we started to develop a number of tools for metabolomics data processing and analysis. Within our prior knowledge processing framework, OmniPath, we provide access to database knowledge about metabolites, drug compounds and metabolism, and we create utilities to make use of this knowledge in data processing and analysis. In this page we maintain a list of our already available tools and resources.

MetaProViz: preprocessing, analysis and visualization

    Git repo  |  Docs

The MetaProViz R package is a collection of utilities for metabolomics data analysis. These include quality control, identifier translation, differential analysis, functional enrichment analysis, and a set of versatile, publication quality visualizations.

COSMOS: multi-omics causal modelling

    Git repo  |  Docs  |  Paper

The COSMOS method, implemented in the cosmosR R/Bioconductor package, combines multiple omics by inferring molecular activities from each omics modality, and mapping the activities to a causal network covering both signalling and metabolism. In the preprint linked above, we present the application of the method in rich case studies.

MetalinksDB: metabolite-protein ligand-receptor interactions

    Git repo  |  Web app  |  Paper

MetalinksDB is an integrated database of interactions between edogenous, small molecule ligands and proteins. Using its web application, it is contextualisable by subcellular location, tissue, biospecimen and pathway.

Pypath: database access and identifier translation

    Git repo  |  Docs  |  Database clients  |  ID translation

The pypath.inputs module includes Python clients for almost 200 databases. Metabolomics related databases include HMDB, RaMP, SwissLipids, Lipid Maps LMSD and PubChem. The pypath.utils.mapping module supports identifier translation, using HMDB and RaMP identifier translation data.

OmnipathR: database access and identifier translation

    Git repo  |  Docs

The OmnipathR R/Bioconductor package provides direct access to several databases, such as HMDB, RaMP, the Chalmers Sysbio GEMs and STITCH. It also supports identifier translation, and contains utilities to build the prior knowledge network for COSMOS.