pyiomica
PyIOmica (pyiomica) is a Python package for omics analyses.
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 7 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.4%) to scientific vocabulary
Keywords
Repository
PyIOmica (pyiomica) is a Python package for omics analyses.
Basic Info
- Host: GitHub
- Owner: gmiaslab
- License: other
- Language: Python
- Default Branch: master
- Homepage: https://pyiomica.readthedocs.io/en/latest/
- Size: 451 MB
Statistics
- Stars: 15
- Watchers: 1
- Forks: 4
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
PyIOmica (pyiomica)
This repository contains PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets. PyIOmica extends MathIOmica usage to Python and implements new visualizations and computational tools for graph analyses. The documentation is available at Read the Docs: https://pyiomica.readthedocs.io/en/latest/
PyIOmica Installation Instructions
A. INSTALLATION
Pre-Installation Requirements
To install PyIOmica on any platform you need Python. Required package dependencies are listed in the setup.py file. The software has been tested with Python 3.13.5. Compatibility with earlier Python 3.x versions depends on the minimum requirements of the dependencies listed in setup.py.
Installation Instructions
- To install the current release from PyPI (Python Package Index) use pip:
bash
pip install pyiomica
Alternatively, you can install directly from github using:
bash
pip install git+https://github.com/gmiaslab/pyiomica/
or
bash
git clone https://github.com/gmiaslab/pyiomica/
python setup.py install
B. RUNNING PyIOmica
After installation you can run:
```python
import pyiomica ```
C. DOCUMENTATION
Documentation for PyIOmica is built-in and is available through the help() functionality in Python. Also the documentation is available at Read the Docs: https://pyiomica.readthedocs.io/en/latest/
D. ADDITIONAL INFORMATION
- PyIOmica is a multi-omics analysis framework distributed as a Python package that aims to assist in bioinformatics.
- The most current version of the package is maintained at https://github.com/gmiaslab/pyiomica
- News are distributed via twitter (@mathiomica)
E. LICENSING
PyIOmica is released under an MIT License. Please also consult the folder LICENSES distributed with PyIOmica regarding Licensing information for use of external associated content.
F. OTHER CONTACT INFORMATION
- G. Mias Lab (https://georgemias.org)
- e-mail: mathiomica@gmail.com
- twitter: @mathiomica
G. FUNDING
PyIOmica development and associated research were supported by the Translational Research Institute for Space Health through NASA Cooperative Agreement NNX16AO69A (Project Number T0412, PI: Mias). The content is solely the responsibility of the authors and does not necessarily represent the official views of the supporting funding agencies.
I. CITATIONS
If you use PyIOmica in your work please use the following citation:
- Sergii Domanskyi, Carlo Piermarocchi and George I Mias, PyIOmica: longitudinal omics analysis and trend identification. Bioinformatics, 36(7), 23062307 (2020). https://doi.org/10.1093/bioinformatics/btz896
If you use PyIOmica's visibility graph functionality, please also consider the following citation:
- Minzhang Zheng, Sergii Domanskyi, Carlo Piermarocchi, and George I Mias, Visibility graph based temporal community detection with applications in biological time series, Sci Rep 11, 5623 (2021). https://doi.org/10.1038/s41598-021-84838-x
Owner
- Name: G. Mias Lab
- Login: gmiaslab
- Kind: user
- Website: georgemias.org
- Repositories: 3
- Profile: https://github.com/gmiaslab
GitHub Events
Total
- Release event: 1
- Push event: 10
- Create event: 1
Last Year
- Release event: 1
- Push event: 10
- Create event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Domanskyi | s****i@g****m | 111 |
| G. Mias Lab | g****b | 59 |
| George Mias | g****b@g****m | 12 |
| zefer001 | 4****1 | 6 |
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 0
- Total pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: about 4 hours
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- MZZheng (4)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 108 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 22
- Total maintainers: 2
pypi.org: pyiomica
Omics Analysis Tool Suite
- Homepage: https://github.com/gmiaslab/pyiomica
- Documentation: https://pyiomica.readthedocs.io/
- License: MIT
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Latest release: 1.4.1
published 8 months ago