https://github.com/alleninstitute/sciduck
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
2 of 4 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 (9.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- Language: Jupyter Notebook
- Default Branch: main
- Size: 30.3 MB
Statistics
- Stars: 2
- Watchers: 5
- Forks: 4
- Open Issues: 5
- Releases: 2
Metadata Files
README.md
sciduck: single cell data quality control toolkit
sciduck provides a transparent framework for single cell/nuclei quality control and annotation. The package was built following anndata and scanpy to easily fit into related workflows. It provides tranparency to single cell analysis pipelines for reproducible data analysis and annotation. The Python-based implementation efficiently deals with
datasets of more than one million cells.
Tutorials:
In the Quality Control tutorial we showcase how to perform various range and group contraints.
In the Plotting tutorial we show how to use the sciduck plotting functions to identify quality control cuttoffs.
In the Annotation Table tutorial we show how to build an annotation table for use in taxonomy development. Typically what is hosted on google sheets at the Allen Institute.
Documentation
Installation
pip install sciduck
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Create event: 6
- Release event: 1
- Issues event: 9
- Member event: 1
- Issue comment event: 5
- Push event: 34
- Pull request review event: 2
- Pull request event: 8
- Fork event: 2
Last Year
- Create event: 6
- Release event: 1
- Issues event: 9
- Member event: 1
- Issue comment event: 5
- Push event: 34
- Pull request review event: 2
- Pull request event: 8
- Fork event: 2
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 12
- Total pull requests: 11
- Average time to close issues: about 2 months
- Average time to close pull requests: 1 day
- Total issue authors: 1
- Total pull request authors: 4
- Average comments per issue: 0.17
- Average comments per pull request: 0.64
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 12
- Pull requests: 11
- Average time to close issues: about 2 months
- Average time to close pull requests: 1 day
- Issue authors: 1
- Pull request authors: 4
- Average comments per issue: 0.17
- Average comments per pull request: 0.64
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- UCDNJJ (12)
- mtvector (1)
Pull Request Authors
- UCDNJJ (6)
- mtvector (5)
- dyuan1111 (2)
- nkempynck (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 27 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 13
- Total maintainers: 1
pypi.org: sciduck
single cell data analyis unification and communication toolkit
- Documentation: https://sciduck.readthedocs.io/
- License: MIT License
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Latest release: 0.5.5
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- anndata *
- numpy *
- scanpy *
- sphinx ==8.0.2
- sphinx_rtd_theme ==3.0.0rc1
- anndata >=0.8
- numpy >=1.23
- pandas >=1.5
- scipy >=1.8
- anndata *
- numpy *
- scanpy *