OmicsLonDA

OmicsLonDA is a software tool to analyze longitudinal omics data collected over time and across large cohorts. It uses a semi-parametric approach to identify time intervals of differential regulation of omics features. The tool is specifically designed to handle inconsistencies in longitudinal data, such as nonuniform sampling intervals, missing data points, subject dropout, and differing numbers of samples per subject. The method used by OmicsLonDA is based on smoothing splines and an empirical distribution constructed through a permutation procedure. The tool has been benchmarked on five simulated datasets and shown to be highly specific and sensitive. It has also been applied to real-world datasets, revealing temporal patterns of amino acids, lipids, and hormone metabolites that are differentially regulated in male versus female subjects following a respiratory infection, as well as potential lipid markers that are temporally significantly different between pregnant women with and without preeclampsia.