DESCRIPTION

Package: lilikoi
Type: Package
Title: Metabolomics Personalized Pathway Analysis Tool
Version: 2.1.0
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: 7.1.1
VignetteBuilder: knitr
Suggests: knitr, rmarkdown