Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
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.
Article activity feed
-
Now published in GigaScience doi: 10.1093/gigascience/giy136
Fadhl M. Al-Akwaa 2Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fadhl M. Al-AkwaaSijia Huang 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLana X. Garmire 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at …
Now published in GigaScience doi: 10.1093/gigascience/giy136
Fadhl M. Al-Akwaa 2Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fadhl M. Al-AkwaaSijia Huang 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLana X. Garmire 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Lgarmire@cc.hawaii.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy136 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101473 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101474 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101475
-
-
