# MetaboDirect
[](https://zenodo.org/badge/latestdoi/356707576)
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](https://pypi.org/project/metabodirect/0.1.1/) using:
```
pip install metabodirect
```
Additionally it can be installed from source by cloning its [GitHub repository](https://github.com/Coayala/MetaboDirect)
```
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
- ggvenn
- vegan
- KEGGREST
- factoextra
- UpSetR
- pmartR (for normalization tests)
- SYNCSA
- ggvenn
### 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](https://metabodirect.readthedocs.io/en/latest/index.html#).
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