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ADViSELipidomics user manual

2 Install

ADViSELipidomics is a stand-alone Shiny application developed in RStudio IDE (RStudio > 1.4) and implemented using the R language (R > 4.0), available at the following GitHub page: https://github.com/ShinyFabio/ADViSELipidomics. ADViSELipidomics is multi-platform. We tested its functionalities on the main operating systems: Windows 10, Windows 11, macOS 12, Ubuntu 18, and Ubuntu 20. The user must first install R (https://www.r-project.org) and R studio (https://www.rstudio.com), if not yet available. Then, before installing ADViSELipidomics, the user might need to perform a few supplementary steps that depend on the operating systems:

  • Windows Install Rtools, a collection of tools necessary for building R packages in Windows, available at the following link: https://cran.r-project.org/bin/windows/Rtools

  • MacOS The following code should be written in the console:

brew install imagemagick@6
brew install cairo
  • Ubuntu The following code should be written in the console:

If you are on Ubuntu run the following codes in the console:

sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo apt-get install libcairo2-dev
sudo apt-get install libxt-dev
sudo apt install libmagick++-dev
sudo apt-get install libc6
sudo apt-get install libnlopt-dev

Then, for all the operating systems, ADViSELipidomics can be installed by typing the following code in the RStudio console:

if(!require("devtools")){
  install.packages("devtools")
}
library(devtools)
install_github("ShinyFabio/ADViSELipidomics")

We kindly suggest updating all the R packages requested during the installation process of ADViSELipidomics Shiny application. Be careful that if you need to install many packages and you decide to use compilation, the process could take a lot depending on your hardware and operating system. Finally to execute ADViSELipidomics the user can type the following code in the RStudio console:

NOTE
Depending on the screen size and especially the resolution of your monitor, ADViSELipidomics interface can be a bit different from how it was thought and built. Try to reduce or increment the zoom using Ctrl +/Ctrl - for Windows or Linux users, or Command +/Command - for Mac users.

Finally, when a new ADViSELipidomics version is released, it can be updated with the same code for the installation.