Metabocano

Description 📑

The Shiny App for making an enhanced interactive volcano plot for metabolomics studies.

• Directly reads the output peak table from mzMine, xcms, MS-DIAL, and Default format (see examples of inputs)
• Merges with the annotation table from SIRIUS
• Intersects peak table with the annotation table from SIRIUS, and Pairs List from GNPS
• Performs imputation by noise, and statistical tests by group pairs
• Generates several outputs:
  • interactive Plotly-type volcano plot with built-in filters
  • table reformatted for MetaboAnalyst input
  • zip archive for AutoPlotter Compounds in Columns input
  • table with statistics and SIRIUS annotation, which can be merged in Cytoscape

Launch the App 🚀

Shiny deployment
https://plyush1993.shinyapps.io/Metabocano/

Run locally
Install:

if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
if (!require("remotes", quietly = TRUE)) {
    install.packages("remotes")
}
remotes::install_github("plyush1993/metabocano", INSTALL_opts = "--no-multiarch")

or

if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pak("plyush1993/metabocano")

Run:

metabocano::run_metabocano()

Important

The App's script was compiled using R version 4.1.2

Contact 📬

Please send any comment, suggestion or question you may have to the author (Dr. Ivan Plyushchenko):