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Analyze FT-ICR-MS data

Project description

MetaboDirect

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

Installation

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 https://github.com/Coayala/MetaboDirect.git
cd MetaboDirect
python setup.py install

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

Python

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

R

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

Cytoscape

  • FileTransfer

Usage

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

metabodirect -h

For more information please check the User Manual.

Project details


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