shedding-hub
Data and statistical models for biomarker shedding.
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com, zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Keywords
Repository
Data and statistical models for biomarker shedding.
Basic Info
- Host: GitHub
- Owner: shedding-hub
- Language: Python
- Default Branch: main
- Homepage: https://shedding-hub.github.io
- Size: 38.7 MB
Statistics
- Stars: 14
- Watchers: 1
- Forks: 2
- Open Issues: 16
- Releases: 1
Topics
Metadata Files
README.md
Shedding Hub 
The Shedding Hub collates data and statistical models for biomarker shedding (such as viral RNA or drug metabolites) in different human specimen (such as stool or sputum samples). Developing wastewater-based epidemiology into a quantitative, reliable epidemiological monitoring tool motivates the project.
Datasets are extracted from appendices, figures, and supplementary materials of peer-reviewed studies. Each dataset is stored as a .yaml file and validated against our data schema to verify its integrity.
📊 Getting the Data
You can obtain the data by downloading it from GitHub. We also provide a convenient Python package so you can download the most recent data directly in your code or obtain a specific version of the data for reproducible analysis. Install the package by running pip install shedding-hub from the command line. The example below downloads the data from Wölfel et al. (2020) as of the commit 259ca0d.
```python
import shedding_hub as sh
sh.load_dataset('woelfel2020virological', ref='259ca0d') {'title': 'Virological assessment of hospitalized patients with COVID-2019', 'doi': '10.1038/s41586-020-2196-x', ...}
```
🤝 Contributing
Thank you for contributing your data to the Shedding Hub and supporting wastewater-based epidemiology! If you hit a bump along the road, create a new issue and we'll sort it out together.
We use pull requests to add and update data, allowing for review and quality assurance. Learn more about the general workflow here. To contribute your data, follow these easy steps (if you're already familiar with pull requests, steps 2 and 3 are for you):
- Create a fork of the Shedding Hub repository by clicking here and clone the fork to your computer. You only have to do this once.
- Create a new
my_cool_study/my_cool_study.yamlfile in thedatadirectory and populate it with your data. See here for a comprehensive example from Wölfel et al. (2020). A minimal example for studies with a single analyte (e.g., SARS-CoV-2 RNA concentration in stool samples) is available here, and a minimal example for studies with multiple analytes (e.g., crAssphage RNA concentration in stool samples and caffeine metabolites in urine) is available here. - Optionally, if you have a recent version of Python installed, you can validate your data to ensure it has the right structure before contributing it to the Shedding Hub.
- Run
pip install -r requirements.txtfrom the command line to install all the Python packages you need. - Run
pytestfrom the command line to validate all datasets, including the one you just created.
- Run
- Create a new branch by running
git checkout -b my_cool_study. Branches let you isolate changes you are making to the data, e.g., if you're simultaneously working on adding multiple studies–much appreciated! You should create a new branch from themainbranch for each dataset you contribute; see here for more information. - Add your changes by running
git add data/my_cool_study/my_cool_study.yamland commit them by runninggit commit -m "Add data from Someone et al. (20xx).". Feel free to pick another commit message if you prefer. - Push the dataset to your fork by running
git push origin my_cool_study. This will send the data to GitHub, and the output of the command will include a lineCreate a pull reuqest for 'my_cool_study' on GitHub by visiting: https://github.com/[your-username]/shedding-hub/pull/new/my_cool_study. Click on the link and follow the next steps to create a new pull request.
Congratulations, you've just created your first pull request to contribute a new dataset! We'll now review the changes you've made to make sure everything looks good. Once any questions have been resolved, we'll merge your changes into the repository. You've just contributed your first dataset to help make wastewater-based epidemiology a more quantitative public health monitoring tool–thank you!
Owner
- Name: Shedding Hub
- Login: shedding-hub
- Kind: organization
- Location: United States of America
- Repositories: 1
- Profile: https://github.com/shedding-hub
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this dataset, please cite it as below along with the primary data sources." type: dataset authors: - family-names: "Wang" given-names: "Yuke" orcid: "https://orcid.org/0000-0002-9615-7859" - family-names: "Hoffmann" given-names: "Till" orcid: "https://orcid.org/0000-0003-4403-0722" - family-names: "Xiao" given-names: "Wenfei" - family-names: "Hu" given-names: "Youwei" - family-names: "Chen" given-names: "Zirui" - family-names: "Zhang" given-names: "Haisu" - family-names: "Shen" given-names: "Lejun" - family-names: "Zhai" given-names: "Siyu" title: "Shedding Hub" version: 1.0.0 doi: 10.5281/zenodo.15052773 date-released: 2025-03-19 url: "https://github.com/shedding-hub/shedding-hub"
GitHub Events
Total
- Create event: 64
- Release event: 1
- Issues event: 46
- Watch event: 10
- Delete event: 52
- Member event: 2
- Issue comment event: 112
- Push event: 500
- Pull request review comment event: 272
- Pull request review event: 262
- Pull request event: 120
- Fork event: 1
Last Year
- Create event: 64
- Release event: 1
- Issues event: 46
- Watch event: 10
- Delete event: 52
- Member event: 2
- Issue comment event: 112
- Push event: 500
- Pull request review comment event: 272
- Pull request review event: 262
- Pull request event: 120
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 37
- Total pull requests: 94
- Average time to close issues: about 1 month
- Average time to close pull requests: 6 days
- Total issue authors: 7
- Total pull request authors: 8
- Average comments per issue: 0.54
- Average comments per pull request: 1.3
- Merged pull requests: 65
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 27
- Pull requests: 83
- Average time to close issues: about 1 month
- Average time to close pull requests: 6 days
- Issue authors: 7
- Pull request authors: 8
- Average comments per issue: 0.44
- Average comments per pull request: 1.23
- Merged pull requests: 55
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- WenfeiXiao (12)
- tillahoffmann (8)
- YWAN446 (7)
- LivZHAI (3)
- hww228 (3)
- lejuncathy (2)
- haisuzhang (2)
Pull Request Authors
- tillahoffmann (29)
- WenfeiXiao (17)
- hww228 (17)
- YWAN446 (14)
- haisuzhang (7)
- ReinaChenzr (5)
- LivZHAI (4)
- lejuncathy (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 7 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 2
pypi.org: shedding-hub
Data and statistical models for biomarker shedding.
- Documentation: https://shedding-hub.readthedocs.io/
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Latest release: 0.1.1
published 6 months ago