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
• statsmodels

R

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

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.