lilikoi: Metabolomics Personalized Pathway Analysis Tool
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>.
| Version: | 2.1.1 |
| 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 |
| Suggests: | knitr,rmarkdown |
| Published: | 2022-10-05 |
| DOI: | 10.32614/CRAN.package.lilikoi |
| 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 at gmail.com> |
| License: | GPL-2 |
| NeedsCompilation: | no |
| Citation: | lilikoi citation info |
| Materials: | README,NEWS |
| In views: | MissingData,Omics |
| CRAN checks: | lilikoi results |
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