PhenomeDB is a platform for integrative storage and analysis of metabolomics data, with tools for creating and running data processing pipelines, harmonisation of metadata, querying/generating integrated cohorts, and analysing and visualising those cohorts using commonly used statistical analyses, including PCA, PCPR2, and MWAS.
Please see the readthedocs website for full documentation, including installation and usage: https://phenomedb.readthedocs.io/en/latest/