TODO list

[x] Download module. pdf format. before Oct 07, 2024
[x] TBtools plugin test. before Oct 07, 2024
[ ] Semi-annotation.
[ ] Move the steps requiring a crawler to a separate panel.
[ ] HTML type report for entire workflow.

Cookbook

MetMiner cookbook: https://shawnwx2019.github.io/metminer-cookbook/

更详细的中文说明: 我的博客

Quick start

Install

##> for chinese users:
##> options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))

if (!require('remotes')) install.packages('remotes');
if (!require('Hmisc')) install.packages('Hmisc');
if (!require('tidymass')) {
  source("https://www.tidymass.org/tidymass-packages/install_tidymass.txt");
  install_tidymass(from = "tidymass.org")
};
if (!require('ropls')) remotes::install_github("SamGG/ropls");
if (!require('PCAtools')) remotes::install_github('kevinblighe/PCAtools');
if (!require('MDAtoolkits')) remotes::install_github('ShawnWx2019/MDAtoolkits',ref = 'master');
if (!require('shinyFiles')) remotes::install_github('thomasp85/shinyFiles');
if (!require('shinyWidgets')) remotes::install_github("dreamRs/shinyWidgets");
if (!require('ComplexHeatmap')) remotes::install_github('jokergoo/ComplexHeatmap');
if (!require('clusterProfiler')) remotes::install_github('YuLab-SMU/clusterProfiler');
if (!require('shinyjs')) install.packages('shinyjs');
if (!require('dashboardthemes')) install.packages('dashboardthemes');
if (!require("DT")) install.packages('DT');
if (!require('shiny')) install.packages('shiny');
if (!require('bsicons')) install.packages('bsicons');
if (!require('bslib')) install.packages('bslib');
if (!require('ggsci')) install.packages('ggsci');
if (!require('plotly')) install.packages('plotly');
if (!require('ggrepel')) install.packages('ggrepel');
if (!require('shinythemes')) install.packages('shinythemes');
if (!require('ggstatsplot')) install.packages('ggstatsplot');
if (!require('patchwork')) install.packages('patchwork');
if (!require('tidyverse')) install.packages('tidyverse');
if (!require('shinyjqui')) install.packages('shinyjqui');
if (!require('colourpicker')) install.packages('colourpicker');
if (!require('RCurl')) install.packages('RCurl');
if (!require('MetMiner')) remotes::install_github('ShawnWx2019/MetMiner');

Start

library(tidyverse)
library(tidymass)
library(MDAtoolkits)
library(MetMiner)
##> start metMiner shinyapp
run_metMiner(maxRequestSize = 300)

Demo

You can download demo file at:

Citation

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

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

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.

If you started metMiner from TBtools plugin, please also cite:

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.

Update

Nov 6, 2024. Version 1.0.0 => Version 1.0.1

Add download button for figures，format: pdf,tiff,png,jpg;
Fix bug for compound classification part;

ShawnWx2019 / MetMiner

readme