SysMet consists of omics tools that can be assembled into a pipeline to help uncover the relationships between diseases and analytes. The Differential Analysis Tool applies statistical and network-based methods to build a differential network. Network activity score is calculated for each analyte to identify disease-associated analytes. The Omics Integration Tool allows integration of multi-omics data acquired from the same set of samples. Integrated network is used to update the network activity scores to investigate disease-associated analytes at the systems level.