MetaboCensoR

Description 📑

The R Shiny App for filtering redundant features in LC-MS peak table and .mgf file.

• Read the output peak table from mzMine, xcms, MS-DIAL, and Default format.
  Check compatibility with examples of inputs.
  • Filter features detected in blank sample group(s) with a widget.
  • Filter Isotopes/Dimers, Adducts, Neutral Loses, In-Source Fragments, Mispicked Ions & Saturated (Ringing) Ions, and generate annotation tables.
  • Filter features by Zero, RSD, Mean, and Min values using selectable logical rules with a widget.
  • Filter peaks by m/z, RT, RMD, AMD bounds and a target peak list to remove/keep with a widget.
• Compile the final filtered peak table, and filter MGF file according to the final peak table.
• Instructions, references, and details.

💡Learn More: Check out the Tutorial for a full GUI walkthrough.
📖Manuscript: Read our Publication for the detailed methodology and performance benchmarking.
🧪Case Studies: Visit the Examples repository for application examples.

Server GUI Map  

Launch the App 🚀

Shiny Web Deployment
plyush1993.shinyapps.io/MetaboCensoR

Install Locally

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

or

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

Run Locally

MetaboCensoR::run_metabocensor()

Alternatively, Windows users can launch the app automatically using a .bat file. After installing R, and MetaboCensoR, edit the batch file so that REXE points to your Rscript.exe.

Important

R 4.5.0
SESSION INFO
CHANGELOG

Citation 🔗

If you use MetaboCensoR, please cite:

Plyushchenko I.V. & Luzzatto-Knaan T. "MetaboCensoR: A Shiny Application for Data Filtering in Untargeted LC-MS Metabolomics to Enhance Interpretability" bioRxiv 2026.07.02.735197

Contact 📬