{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/lilikoi-an-r-package-for-personalized-pathway","title":"Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data","arxiv_id":null,"date":"2018-07-18","proceeding":null,"authors":["Fadhl M AlAkwaa","Breck Yunits","Sijia Huang","Hassam Alhajaji","Lana X Garmire"],"abstract":"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. The package is freely available under the GPLv3 license through the github repository at: https://github.com/lanagarmire/lilikoi and CRAN: https://cran.r-project.org/web/packages/lilikoi/index.html.","url_abs":"https://academic.oup.com/gigascience/article/7/12/giy136/5237705","url_pdf":"https://academic.oup.com/gigascience/article-pdf/7/12/giy136/28878201/giy136.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"lilikoi-an-r-package-for-personalized-pathway","repo_url":"https://github.com/lanagarmire/lilikoi","is_official":0,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"classification-1","task_name":"Classification"},{"task_slug":"classification","task_name":"General Classification"},{"task_slug":"feature-selection","task_name":"feature selection"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}