Abstract
MOTIVATION: Lipidomics is a rapidly expanding field focused on studying lipid species and classes within biological systems. As the field evolves, there is an increasing demand for user-friendly, open-source software tools capable of handling large and complex datasets while keeping pace with technological advancements. LipidSig, a widely used web-based platform, has been instrumental in data analysis and visualization of lipidomics. However, its limitations become evident when users want to build customized workflows. To address the limitation, we developed a companion R package, LipidSigR, based on the R code of the LipidSig web platform. RESULTS: LipidSigR offers greater flexibility, allowing researchers with basic R programming skills to modify and adapt workflows according to their needs. It has been rigorously tested following CRAN guidelines to ensure compatibility and reproducibility. In demonstrating its functionality, we analyze the case with commonly used experimental design, case versus control, in lipidomics studies. Researchers can follow the use case to explore the key capabilities and build customized lipidomics data analysis workflows using LipidSigR. AVAILABILITY AND IMPLEMENTATION: LipidSigR is freely available from https://lipidsig.bioinfomics.org/lipidsigr/index.html and https://github.com/BioinfOMICS/LipidSigR.