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
- 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.
1 maintainer
Metadata
1 maintainer
Release files for metabodirect 0.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| metabodirect-0.3.2.tar.gz | 3.2 MB | Without provenance | Details for metabodirect-0.3.2.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| metabodirect-0.3.2-py3-none-any.whl | Python 3 | none | any | Details for metabodirect-0.3.2-py3-none-any.whl |
Total release size: 6.5 MB
Release files / metabodirect-0.3.2.tar.gz
| Download URL | metabodirect-0.3.2.tar.gz |
|---|---|
| Size | 3.2 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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twine/3.4.1 importlib_metadata/4.5.0 pkginfo/1.6.1 requests/2.24.0 requests-toolbelt/0.9.1 tqdm/4.50.2 CPython/3.8.5
|
Release files / metabodirect-0.3.2-py3-none-any.whl
| Download URL | metabodirect-0.3.2-py3-none-any.whl |
|---|---|
| Size | 3.3 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/3.4.1 importlib_metadata/4.5.0 pkginfo/1.6.1 requests/2.24.0 requests-toolbelt/0.9.1 tqdm/4.50.2 CPython/3.8.5
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Security for metabodirect 0.3.2
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