https://github.com/brickmanlab/cat-python
Cluster Alignment Tool (CAT)
Science Score: 26.0%
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
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✓DOI references
Found 5 DOI reference(s) in README -
○Academic publication links
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○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 (9.2%) to scientific vocabulary
Keywords
Repository
Cluster Alignment Tool (CAT)
Basic Info
- Host: GitHub
- Owner: brickmanlab
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://brickmanlabcat.readthedocs.io
- Size: 4.36 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Cluster Alignment Tool (CAT)
Installation
console
$ pip install cat-python
Installation from source
console
$ pip install git+https://github.com/brickmanlab/cat-python.git@master
Running CAT
console
$ catcli \
--ds1 ./tests/datasets/mock.h5ad \
--ds1_name DS1 \
--ds1_cluster Condition_E+D \
--ds2 ./tests/datasets/mock.h5ad \
--ds2_name DS2 \
--ds2_cluster Condition_E+D \
--output ./res
Build documentation
console
$ sphinx-build -M html docs docs/_build
Citation
Please consider citing scANVI Explainer if you use in your research.
Rothová, M.M., Nielsen, A.V., Proks, M. et al.
Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomics.
Nat Cell Biol 24, 833–844 (2022). 10.1038/s41556-022-00923-x
```BibTeX @article{rothova2022, title = {Identification of the Central Intermediate in the Extra-Embryonic to Embryonic Endoderm Transition through Single-Cell Transcriptomics}, author = {Rothov{\'a}, Michaela Mrugala and Nielsen, Alexander Valentin and Proks, Martin and Wong, Yan Fung and Riveiro, Alba Redo and {Linneberg-Agerholm}, Madeleine and David, Eyal and Amit, Ido and Trusina, Ala and Brickman, Joshua Mark}, year = {2022}, month = jun, journal = {Nature Cell Biology}, volume = {24}, number = {6}, pages = {833--844}, publisher = {Nature Publishing Group}, issn = {1476-4679}, doi = {10.1038/s41556-022-00923-x} }
```
Owner
- Name: Brickman group
- Login: brickmanlab
- Kind: organization
- Location: Copenhagen
- Website: https://danstem.ku.dk/research1/brickman/
- Repositories: 3
- Profile: https://github.com/brickmanlab
Professor Joshua Brickman at Center for Stem Cell Medicine (reNEW), University of Copenhagen
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 43 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 1
pypi.org: cat-python
Cluster Alignment Tool (CAT)
- Homepage: https://github.com/brickmanlab/cat-python
- Documentation: https://brickmanlabcat.readthedocs.io/
- License: MIT License Copyright (c) 2024, Alex Valentin Nielsen, Martin Proks, Ala Trusina Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 1.1.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout main composite
- astral-sh/setup-uv v2 composite
- actions/checkout main composite
- actions/download-artifact v4 composite
- actions/upload-artifact v4 composite
- astral-sh/setup-uv v2 composite
- pypa/gh-action-pypi-publish release/v1 composite
- anndata *
- plotly *
- polars *
- pyarrow *
- rich *
- rich_argparse *
- xlsxwriter *