https://github.com/cbg-ethz/pmhn
Personalised mutual hazard networks: fixed effects in cancer progression modeling
Science Score: 36.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary
Keywords
Repository
Personalised mutual hazard networks: fixed effects in cancer progression modeling
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://cbg-ethz.github.io/pMHN/
- Size: 4.26 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
Personalised Mutual Hazard Networks
Principled probabilistic modelling with Mutual Hazard Networks.
- Documentation: https://cbg-ethz.github.io/pMHN
- Source code: https://github.com/cbg-ethz/pMHN
- Bug reports: https://github.com/cbg-ethz/pMHN/issues
Running the workflows
To facilitate reproducibility we use Snakemake. We recommend creating a new virtual environment (e.g., using Micromamba) and installing Snakemake as described in their documentation.
Once the environment is set, the package can be installed using
bash
$ pip install -e . # Note -e which will allow modifying the code when needed
Contributing
We use Poetry to control dependencies.
When Poetry is installed, clone the repository and type
bash
$ poetry install --with dev
to install the package with the dependencies used for development.
At this stage you should be able to use Pytest to run unit tests:
bash
$ poetry run pytest
Alternatively, you may want to work inside Poetry environment:
bash
$ poetry shell
$ pytest
When you submit a pull request, automated continuous integration tests will be run. They include unit tests as well as code quality checks. To run the code quality checks automatically at each commit made, we use pre-commit. To activate it run:
bash
$ poetry shell # If it is not already active
$ pre-commit install
Acknowledgements
This package is built around LearnMHN (the backend for Mutual Hazard Networks) and PyMC (probabilistic programming framework).
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
- Issues event: 2
- Delete event: 6
- Push event: 20
- Pull request event: 10
- Create event: 6
Last Year
- Issues event: 2
- Delete event: 6
- Push event: 20
- Pull request event: 10
- Create event: 6
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Paweł Czyż | p****z@a****h | 19 |
| laurenzkeller | 1****r | 8 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 12
- Total pull requests: 47
- Average time to close issues: 5 months
- Average time to close pull requests: 11 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.17
- Average comments per pull request: 1.19
- Merged pull requests: 42
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pawel-czyz (8)
Pull Request Authors
- pawel-czyz (21)
- laurenzkeller (9)