# MetaboDirect
[![DOI](https://zenodo.org/badge/356707576.svg)](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
- 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](https://metabodirect.readthedocs.io/en/latest/index.html#).
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"description": "# MetaboDirect\r\n\r\n[![DOI](https://zenodo.org/badge/356707576.svg)](https://zenodo.org/badge/latestdoi/356707576)\r\n\r\nA comprehensive command-line based pipeline for the analysis of direct injection FT-ICR mass spectrometry data.\r\n\r\n## Installation\r\n\r\nMetaboDirect can be installed directly from [PyPi](https://pypi.org/project/metabodirect/0.1.1/) using:\r\n\r\n```\r\npip install metabodirect\r\n```\r\n\r\nAdditionally it can be installed from source by cloning its [GitHub repository](https://github.com/Coayala/MetaboDirect)\r\n\r\n```\r\ngit clone https://github.com/Coayala/MetaboDirect.git\r\ncd MetaboDirect\r\npython setup.py install\r\n```\r\n\r\nMetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules:\r\n\r\n### Python\r\n\r\n- argparse\r\n- numpy\r\n- pandas\r\n- seaborn\r\n- more-itertools\r\n- py4cytoscape\r\n- statsmodels\r\n\r\n### R\r\n\r\n- tidyverse\r\n- RColorBrewer\r\n- vegan\r\n- ggnewscale\r\n- ggpubr\r\n- KEGGREST\r\n- factoextra\r\n- UpSetR\r\n- pmartR (for normalization tests)\r\n- SYNCSA\r\n- ggvenn\r\n- ggrepel\r\n\r\n### Cytoscape\r\n\r\n- FileTransfer\r\n\r\n## Usage\r\n\r\nInformation about the arguments can be obtaining using the option -h/--help\r\n\r\n```\r\nmetabodirect -h\r\n```\r\nFor more information please check the [User Manual](https://metabodirect.readthedocs.io/en/latest/index.html#).\r\n\r\n\r\n",
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