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: |
2.1.0 |
| 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: |
2022-02-22 |
| 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 |
| CRAN checks: |
lilikoi results |
Documentation:
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