MetMiner cookbook

Large-scale Plant Metabolomics Data Processing and Data Mining

Project

MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis.

This is the documentation of MetMiner. You can get up-to-date verison from the GitHub repository https://github.com/ShawnWx2019/MetMiner.

In this pipeline, tidyMass Shen et al. (2022) take on the majority of the upstream data analysis, data cleaning, and metabolite annotation tasks.

Furthermore, we have developed a Metabolomics Downstream Analysis toolkit MDAtoolkits and a user-friendly WGCNA Shiny app. They are responsible for the downstream analysis and data mining section.

The metMiner shiny app has been packaged into a TBtools Chen et al. (2023) plugin, which can be downloaded and installed through the TBtools plugin store. Thanks to TBtools for providing a convenient dependency resolution solution.

Citation

If you have utilized MetMiner in your project, please cite:

  1. Xiao Wang, Shuang Liang, Wenqi Yang, Ke Yu, Fei Liang, Bing Zhao, Xiang Zhu, Chao Zhou, Luis A. J. Mur, Jeremy A. Roberts, Junli Zhang and Xuebin Zhang. 2024 “MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis.” Journal of Integrative Plant Biology https://doi.org/10.1111/jipb.13774

  2. Shen, Xiaotao, Hong Yan, Chuchu Wang, Peng Gao, Caroline H. Johnson, and Michael P. Snyder. 2022. “TidyMass an Object-Oriented Reproducible Analysis Framework for LC Data.” Nature Communications 13 (1): 4365. https://doi.org/10.1038/s41467-022-32155-w.

References

Chen, Chengjie, Ya Wu, Jiawei Li, Xiao Wang, Zaohai Zeng, Jing Xu, Yuanlong Liu, et al. 2023. “TBtools-II: A "One for All, All for One" Bioinformatics Platform for Biological Big-Data Mining.” Molecular Plant 0 (0). https://doi.org/10.1016/j.molp.2023.09.010.
Shen, Xiaotao, Hong Yan, Chuchu Wang, Peng Gao, Caroline H. Johnson, and Michael P. Snyder. 2022. “TidyMass an Object-Oriented Reproducible Analysis Framework for LC–MS Data.” Nature Communications 13 (1): 4365. https://doi.org/10.1038/s41467-022-32155-w.