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Possbile applications include finding the optimal resolution for\nsingle-cell RNA-sequencing clusterings.\n\n`pyclustree` is inspired by the R package `clustree` ([Github repository](https://github.com/lazappi/clustree)), however, while we aim to provide the same functionality, the API\nwill differ between the implementations.\n\n## Getting started\n\nPlease refer to the [documentation][link-docs].\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system. If you don't have\nPython installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).\n\nThere are several alternative options to install pyclustree:\n\n1. Install the latest release of `pyclustree` from [PyPI][link-pypi]:\n\n```bash\npip install pyclustree\n```\n\n2. Install the latest development version:\n\n```bash\npip install git+https://github.com/complextissue/pyclustree.git@dev\n```\n\n## Contact\n\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Authors\n\n@maltekuehl\n@harryhaller001\n\nUnaffiliated with the creators of the R package `clustree`.\n\n## License\n\nPlease refer to the [LICENSE][license] file.\n\n## Citation\n\nPlease cite both the original R package as well as this implementation when using `pyclustree`. For example: Cluster resolution was determined based on visualization with pyclustree (Kuehl et al., 2024), a Python implementation of clustree (Zappia et al., 2018).\n\n-   pyclustree: Kuehl, M., Hellmig, M., \u0026 Puelles, V. G. (2024). pyclustree: Visualizing cluster resolution optimization for biomedical data (0.3.1). Zenodo. https://doi.org/10.5281/zenodo.13987570\n-   clustree: Zappia, L., \u0026 Oshlack, A. (2018). Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience, 7(7), giy083.\n\n[license]: https://github.com/complextissue/pyclustree/blob/main/LICENSE\n[issue-tracker]: https://github.com/complextissue/pyclustree/issues\n[changelog]: https://pyclustree.readthedocs.io/latest/changelog.html\n[link-docs]: https://pyclustree.readthedocs.io\n[link-pypi]: https://pypi.org/project/pyclustree\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomplextissue%2Fpyclustree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcomplextissue%2Fpyclustree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomplextissue%2Fpyclustree/lists"}