Understanding the Lipidome at the Systems Level with lipidomeR

Lipidomics is one of the fastest-growing areas of molecular profiling in medicine. While increasing amounts of lipidomics data are generated, tools for analyzing and interpreting these data are not equally widely available. We present the lipidomeR -- a tool specifically designed for systematic interpretation of large lipidome-wide studies. The lipidomeR binds together statistical analysis and high-dimensional visualization, providing a reproducible pipeline for rapid interpretation of the lipidome via integrative publication-ready figures. The lipidomeR package is available through the Comprehensive R Archive (CRAN). We demonstrate the lipidomeR with three studies from the Metabolomics Workbench repository, ranging from the human plasma reference material to breast tumor tissue and to the progression of non-alcoholic liver disease (NAFLD) in the liver. In these studies, lipidomeR reveals a diversity of lipidomic patterns, both, within and between the lipid classes as well as over the stages of progression of the diseases.