https://github.com/cbg-ethz/scatrex
Map single-cell transcriptomes to copy number evolutionary trees.
Science Score: 57.0%
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 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 1 committers (100.0%) from academic institutions -
✓Institutional organization owner
Organization cbg-ethz has institutional domain (www.bsse.ethz.ch) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.7%) to scientific vocabulary
Keywords
Repository
Map single-cell transcriptomes to copy number evolutionary trees.
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://www.biorxiv.org/content/10.1101/2021.11.04.467244v1
- Size: 4.95 MB
Statistics
- Stars: 13
- Watchers: 3
- Forks: 1
- Open Issues: 3
- Releases: 3
Topics
Metadata Files
README.md
Map single-cell transcriptomes to copy number evolutionary trees. Check out the tutorial for more information.
Installation
$ pip install scatrex
SCATrEx uses JAX to perform automatic differentiation. By default, SCATrEx installs the CPU-only version of JAX, but we strongly recommend the use of GPU acceleration. Please follow the instructions in https://github.com/google/jax#pip-installation-gpu-cuda to install the GPU version of JAX.
Preprint
https://doi.org/10.1101/2021.11.04.467244
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
Last Year
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| pedrofale | p****a@b****h | 608 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 3
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- 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
- pedrofale (2)
- nhuhoa (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 20 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 5
- Total maintainers: 1
pypi.org: scatrex
Map single-cell transcriptomes to copy number evolutionary trees.
- Homepage: https://github.com/cbg-ethz/SCATrEx
- Documentation: https://scatrex.readthedocs.io/
- License: GNU GENERAL PUBLIC LICENSE 3
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Latest release: 0.2.0
published almost 4 years ago
Rankings
Maintainers (1)
Dependencies
- black ^22.3.0 develop
- bump2version ^1.0.1 develop
- pytest ^6.2.4 develop
- anndata ^0.7.5
- graphviz ^0.14.1
- gseapy ^0.10.5
- jax 0.2.20
- jaxlib 0.1.71
- networkx ^2.6.2
- numpy ^1.21.2
- pandas ^1.3.2
- pybiomart ^0.2.0
- pygraphviz ^1.7
- python >=3.7.1,<3.10
- scanpy ^1.7.0
- scikit-learn ^0.23.2
- scipy ^1.7.3
- tqdm ^4.57.0
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish master composite
- snok/install-poetry v1 composite
- ts-graphviz/setup-graphviz v1 composite