HPC_tidymass

Pipeline for processing large scale untargeted metabolomics data using Tidymass on Ubuntu 20.04 server.

Getting started

Dependence

R version: >4.1.1

OS: MacOS > 10.10, Win 7-11, Ubuntu 20.04

Warning

Only Ubuntu 20.04 has passed the test. Other Linux distributions need to be tested.

Dependence

LC-MS data analysis framwork: TidyMass developed by Dr. Xiaotao Shen. [^1]

if(!require(remotes)){
install.packages("remotes")
}
remotes::install_gitlab("tidymass/tidymass")

Metabolomics Downstream Analysis toolkits: MDAtoolkits

## install from github
suppressMessages(if (!require('MDAtoolkits')) install_github(repo = "ShawnWx2019/MDAtoolkits",ref = 'master'))
## two functions from another package called IMOtoolkits. will be intergreted with MDAtoolkits.
suppressMessages(if (!require('IMOtoolkits')) install_github(repo = "ShawnWx2019/IMOtoolkits"))

Untargeted metabolomics upstream analysis pipeline based on tidyMass: HPC-tidymass

##>  you can download this pipeline from github or just clone the repo to your server
##>  1.0 clone the repo to your server
git clone https://github.com/ShawnWx2019/HPC_tidymass.git

##> Run the initialization script to configure the runtime environment.

cd HPC_tidymass && chmod +x init.sh && bash init.sh

##> test
hpc-runTidymass -h

Important

A user-friendly WGCNA Shiny app: WGCNA-shinyApp follow the steps of WGCNA-shinyapp readme file