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
- 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.
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