https://github.com/cytomining/copairs
Find profile pairs and compute metrics between them.
Science Score: 49.0%
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
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 7 committers (28.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Keywords from Contributors
Repository
Find profile pairs and compute metrics between them.
Basic Info
- Host: GitHub
- Owner: cytomining
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://doi.org/10.1038/s41467-025-60306-2
- Size: 2.13 MB
Statistics
- Stars: 19
- Watchers: 6
- Forks: 9
- Open Issues: 14
- Releases: 16
Metadata Files
README.md
# copairs
copairs is a Python package for finding groups of profiles based on metadata and calculate mean Average Precision to assess intra- vs inter-group similarities.
Getting started
System requirements
copairs supports Python 3.8+ and should work with all modern operating systems (tested with MacOS 13.5, Ubuntu 18.04, Windows 10).
Dependencies
copairs depends on widely used Python packages: * numpy * pandas * tqdm * statsmodels * [optional] plotly
Installation
To install copairs and dependencies, run:
bash
pip install copairs
To also install dependencies for running examples, run:
bash
pip install copairs[demo]
Testing
To run tests, run:
bash
pip install -e .[test]
pytest
Usage
We provide examples demonstrating how to use copairs for: - grouping profiles based on their metadata - calculating mAP to assess phenotypic activity of perturbations - calculating mAP to assess phenotypic consistency of perturbations - estimating null size for mAP p-value calculation
Citation
If you find this work useful for your research, please cite our paper:
Kalinin, A.A., Arevalo, J., Serrano, E., Vulliard, L., Tsang, H., Bornholdt, M., Muñoz, A.F., Sivagurunathan, S., Rajwa, B., Carpenter, A.E., Way, G.P. and Singh, S., 2025. A versatile information retrieval framework for evaluating profile strength and similarity. Nature Communications 16, 5181. doi:10.1038/s41467-025-60306-2
BibTeX:
@article{kalinin2025versatile,
author = {Kalinin, Alexandr A. and Arevalo, John and Serrano, Erik and Vulliard, Loan and Tsang, Hillary and Bornholdt, Michael and Muñoz, Alán F. and Sivagurunathan, Suganya and Rajwa, Bartek and Carpenter, Anne E. and Way, Gregory P. and Singh, Shantanu},
title = {A versatile information retrieval framework for evaluating profile strength and similarity},
journal = {Nature Communications},
year = {2025},
volume = {16},
number = {1},
pages = {5181},
doi = {10.1038/s41467-025-60306-2},
url = {https://doi.org/10.1038/s41467-025-60306-2},
issn = {2041-1723}
}
Owner
- Name: cytomining
- Login: cytomining
- Kind: organization
- Repositories: 27
- Profile: https://github.com/cytomining
GitHub Events
Total
- Create event: 10
- Issues event: 24
- Release event: 6
- Watch event: 13
- Delete event: 3
- Member event: 3
- Issue comment event: 59
- Push event: 16
- Pull request review comment event: 28
- Pull request event: 23
- Pull request review event: 37
- Fork event: 2
Last Year
- Create event: 10
- Issues event: 24
- Release event: 6
- Watch event: 13
- Delete event: 3
- Member event: 3
- Issue comment event: 59
- Push event: 16
- Pull request review comment event: 28
- Pull request event: 23
- Pull request review event: 37
- Fork event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| John Arevalo | j****o@g****m | 106 |
| alxndrkalinin | 1****n@u****m | 71 |
| Alan Munoz | a****g@g****m | 21 |
| axiomcura | e****3@g****m | 6 |
| Shantanu Singh | s****h@b****g | 3 |
| Alán F. Muñoz | a****o@b****g | 2 |
| jessica-ewald | 3****d@u****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 47
- Total pull requests: 61
- Average time to close issues: 4 months
- Average time to close pull requests: 7 days
- Total issue authors: 9
- Total pull request authors: 6
- Average comments per issue: 0.79
- Average comments per pull request: 1.23
- Merged pull requests: 49
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 16
- Pull requests: 27
- Average time to close issues: 6 days
- Average time to close pull requests: 8 days
- Issue authors: 5
- Pull request authors: 4
- Average comments per issue: 0.56
- Average comments per pull request: 2.7
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- johnarevalo (27)
- alxndrkalinin (9)
- afermg (4)
- shntnu (2)
- axiomcura (1)
- AMCalejandro (1)
- ritvikvasan (1)
- jessica-ewald (1)
- danr (1)
Pull Request Authors
- johnarevalo (25)
- alxndrkalinin (15)
- afermg (11)
- shntnu (5)
- jessica-ewald (4)
- axiomcura (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 272 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 3
pypi.org: copairs
Find pairs and compute metrics between them
- Homepage: https://github.com/cytomining/copairs
- Documentation: https://copairs.readthedocs.io/
- License: bsd-3-clause
-
Latest release: 0.5.1
published about 1 year ago
Rankings
Maintainers (3)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v3 composite
- pandas *
- tqdm *