Package: lilikoi
Type: Package
Title: Metabolomics Personalized Pathway Analysis Tool
Version: 2.1.1
Authors@R: c(
 person("Xinying", "Fang", email = "xinyingf@umich.edu", role = c("aut")),
 person("Yu", "Liu", email = "uiluy@umich.edu", role = "aut"),
 person("Zhijie", "Ren", email = "rzj@umich.edu", role = "aut"),
 person("Fadhl", "Alakwaa", email = "falakwaa@hawaii.edu", role = "aut"),
 person("Sijia", "Huang", email = "scarlettcanny@gmail.com", role = "aut"),
 person("Lana", "Garmire", email = "lana.garmire.group@gmail.com", role = c("aut","cre")))
Description: A comprehensive analysis tool for metabolomics data.  It
        consists a variety of functional modules, including several new
        modules: a pre-processing module for normalization and
        imputation, an exploratory data analysis module for dimension
        reduction and source of variation analysis, a classification
        module with the new deep-learning method and other
        machine-learning methods, a prognosis module with cox-PH and
        neural-network based Cox-nnet methods, and pathway analysis
        module to visualize the pathway and interpret
        metabolite-pathway relationships. References: H. Paul Benton
        <http://www.metabolomics-forum.com/index.php?topic=281.0> Jeff
        Xia
        <https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R>
        Travers Ching, Xun Zhu, Lana X. Garmire (2018)
        <doi:10.1371/journal.pcbi.1006076>.
biocViews:
Depends: R (>= 3.5.0)
Imports: car, caret, dplyr, gbm, ggplot2, glmnet, h2o, impute,
        infotheo, limma, M3C, Metrics, MLmetrics, parallel, princurve,
        pathview, plyr, preprocessCore, pROC, RCy3, reticulate,
        reshape, RWeka, scales, stats, stringr, survminer, survival
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.2.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2026-10-16 07:27:22 UTC; root
Author: Xinying Fang [aut], Yu Liu [aut], Zhijie Ren [aut], Fadhl
        Alakwaa [aut], Sijia Huang [aut], Lana Garmire [aut, cre]
Maintainer: Lana Garmire <lana.garmire.group@gmail.com>
Config/pak/sysreqs: cmake make default-jdk libicu-dev libjpeg-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev python3
        libzmq3-dev zlib1g-dev
Repository: https://granatumx.r-universe.dev
Date/Publication: 2022-10-05 18:00:02 UTC
RemoteUrl: https://github.com/cran/lilikoi
RemoteRef: HEAD
RemoteSha: 1caf63620ae215bfc9fa696b5c96ca8a4191f53f