Lilikoi: An R Package For Personalized Pathway-Based Classification Modeling Using Metabolomics Data

Lilikoi (the Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway-based classification modeling using metabolomics data. Four basic modules are presented as the backbone of the package: feature mapping module, which standardizes the metabolite names provided by users and maps them to pathways; dimension transformation module, which transforms the metabolomic profiles to personalized pathway-based profiles using pathway deregulation scores; feature selection module, which helps to select the significant pathway features related to the disease phenotypes; and classification and prediction module, which offers various machine learning classification algorithms.