Abstract
Backgroundpreviously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, it is important to update Lilikoi software.Resultshere we report the next version of Lilikoi as a significant upgrade. The new Lilikoi v2.0 R package has implemented a deep learning method for classification, in addition to popular machine learning methods. It also has several new modules, including the most significant addition of prognosis prediction, implemented by Cox-proportional hazards model and the deep learning–based Cox-nnet model. Additionally, Lilikoi v2.0 supports data preprocessing, exploratory analysis, pathway visualization, and metabolite pathway regression.ConculsionLilikoi v2.0 is a modern, comprehensive package to enable metabolomics analysis in R programming environment.
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