ADViSELipidomics

ADViSELipidomics is a novel Shiny app for the preprocessing, analysis,
and visualization of lipidomics data. It copes with the outputs from
LipidSearch and LIQUID for lipid identification and quantification, and
with data available from the Metabolomics Workbench. ADViSELipidomics
extracts information by parsing lipid species (using LIPID MAPS
classification) and, together with information available on the samples,
allows performing several exploratory and statistical analyses. In the
presence of internal lipid standards in the experiment, ADViSELipidomics
can normalize the data matrix, providing absolute values of
concentration per lipid and sample. Moreover, it allows the
identification of differentially abundant lipids in simple and complex
experimental designs, dealing with batch effect correction.

Installation

ADViSELipidomics is a stand-alone application implemented using the R
language (R > 4.0) and the Shiny libraries. It can be installed as any
other R package on several operating systems (Windows, macOS and Linux).
Before installing the package you have to perform few supplementary
steps based on your operating systems:

• Windows (tested on Windows 10 64bit) 

On Windows, ADViSELipidomics should work out of the box. If you
encounter some problems during the installation, try to install Rtools
from the following link:

https://cran.r-project.org/bin/windows/Rtools.

• MacOS
  If you are on MacOs run the following codes in the console:

brew install imagemagick@6
brew install cairo

• Ubuntu (tested on 18.04).

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

After that, open RStudio, check if you have already installed the
{devtools} package and run the following code:

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.

Usage

Once the installation is completed, run:

library("ADViSELipidomics")
run_ADViSELipidomics()

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 and + or Ctrl and - for Windows or Linux users, or
Command and + or Command and - for Mac users.

An user manual is available at the following link:
https://shinyfabio.github.io/ADViSELipidomics_book/

Docker

A docker version of ADViSELipidomics is also available. Please, first
install Docker Desktop from here:

https://docs.docker.com/get-docker/

After that, open your console and run this code:

docker run -p 80:80 shinyfabio/adviselipidomics:latest

Finally open your browser (tested on Chrome, Firefox can have some
problems) and go to this link:

http://localhost:80/

Update

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

Data Availability

The software is intended as a tool for analyzing lipidomic data,
nevertheless is it possible to test it with two different case studies
as described in the supplementary to our paper
Supplementary.

If you want to test the software with a LipidSearch output, here we
provide the files used in the Case Study 1. Before use, please extract
the files from the archive.

Case_Study_1.zip

It is also possible to test it with a Metabolomics Workbench lipidomic
experiment. ADViSELipidomics can download in real-time suitable selected
lipidomic experiments from the online repository using the do_query()
function from the {metabolomicsWorkbenchR} package. Internet
connection is required.

Citation

If you use ADViSELipidomics in your publications, we appreciate if you
can cite us:

E. Del Prete et al. (2022) ADViSELipidomics: a workflow for analyzing
lipidomics data. Bioinformatics, 2022, 1–3

Funding

This work was supported by the project “Antitumor Drugs and Vaccines
from the Sea (ADViSE)” project (CUP B43D18000240007–SURF
17061BP000000011) funded by POR Campania FESR 2014-2020 “Technology
Platform for Therapeutic Strategies against Cancer” - Action 1.2.1 and
1.2.2.