Lilikoi V2.0: a deep-learning enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data

Previously we developed Lilikoi , a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, here 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-PH model and the deep-learning based Cox-nnet model. Additionally, Lilikoi v2.0 supports data preprocessing, exploratory analysis, pathway visualization and metabolite-pathway regression. In summary, Lilikoi v2.0 is a modern, comprehensive package to enable metabolomics analysis in R programming environment.