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Analyze FT-ICR-MS data

Project description



A comprehensive command-line based pipeline for the analysis of direct injection FT-ICR mass spectrometry data.


MetaboDirect can be installed directly from PyPi using:

pip install metabodirect

Additionally it can be installed from source by cloning its GitHub repository

git clone
cd MetaboDirect
python install

MetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules:


  • argparse
  • numpy
  • pandas
  • seaborn
  • more-itertools
  • py4cytoscape
  • statsmodels


  • tidyverse
  • RColorBrewer
  • vegan
  • ggnewscale
  • ggpubr
  • ggvenn
  • factoextra
  • UpSetR
  • pmartR (for normalization tests)
  • ggvenn


  • FileTransfer


Information about the arguments can be obtaining using the option -h/--help

metabodirect -h

For more information please check the User Manual.

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