lilikoi: Metabolomics Personalized Pathway Analysis Tool

A personalized metabolites and pathway analysis tool. With the metabolites data provided by users, lilikoi maps the metabolites data into pathways and calculates pathway deregulation scores. It enables users to perform exploratory analysis, classification and prognosis analysis on both metabolites and pathways. References: Fadhl M AlAkwaa, Breck Yunits, Sijia Huang, Hassam Alhajaji, Lana X Garmire <> H. Paul Benton <> Jeff Xia <> Travers Ching, Xun Zhu, Lana X. Garmire (2018) <doi:10.1371/journal.pcbi.1006076>.

Version: 2.0.0
Depends: R (≥ 3.5.0)
Imports: car, caret, dplyr, gbm, ggplot2, glmnet, h2o, impute, infotheo, limma, M3C, Metrics, parallel, pathifier, pathview, plyr, preprocessCore, pROC, RCy3, reticulate, reshape, RWeka, scales, stringr, survminer, survival
Suggests: knitr, rmarkdown
Published: 2020-07-03
Author: Xinying Fang [aut], Yu Liu [aut], Zhijie Ren [aut], Lana Garmire [aut, cre]
Maintainer: Lana Garmire <lgarmire at>
License: GPL-2
NeedsCompilation: no
Materials: README NEWS
CRAN checks: lilikoi results


Reference manual: lilikoi.pdf
Vignettes: Lilikoi V2.0
Package source: lilikoi_2.0.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel: not available
macOS binaries: r-release: lilikoi_0.1.0.tgz, r-oldrel: not available
Old sources: lilikoi archive


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