https://github.com/complextissue/pyclustree
A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
https://github.com/complextissue/pyclustree
clustree pyclustree scverse single-cell
Last synced: 4 months ago
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A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
- Host: GitHub
- URL: https://github.com/complextissue/pyclustree
- Owner: complextissue
- License: gpl-3.0
- Created: 2024-09-15T14:21:13.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-09-10T19:23:43.000Z (9 months ago)
- Last Synced: 2026-02-17T10:55:18.160Z (4 months ago)
- Topics: clustree, pyclustree, scverse, single-cell
- Language: Python
- Homepage: https://pyclustree.readthedocs.io/latest/start.html
- Size: 6.37 MB
- Stars: 13
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# pyclustree
[](https://pypi.org/project/pyclustree/)
[](https://img.shields.io/pypi/l/pyclustree)
[](https://pyclustree.readthedocs.io/stable/?badge=stable)
[](https://codecov.io/gh/complextissue/pyclustree)
[](https://pypi.org/project/pyclustree/)
[](https://doi.org/10.5281/zenodo.13987570)
Visualize cluster assignments at different resolutions. Possbile applications include finding the optimal resolution for
single-cell RNA-sequencing clusterings.
`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
will differ between the implementations.
## Getting started
Please refer to the [documentation][link-docs].
## Installation
You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install pyclustree:
1. Install the latest release of `pyclustree` from [PyPI][link-pypi]:
```bash
pip install pyclustree
```
2. Install the latest development version:
```bash
pip install git+https://github.com/complextissue/pyclustree.git@dev
```
## Contact
If you found a bug, please use the [issue tracker][issue-tracker].
## Authors
@maltekuehl
@harryhaller001
Unaffiliated with the creators of the R package `clustree`.
## License
Please refer to the [LICENSE][license] file.
## Citation
Please 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).
- pyclustree: Kuehl, M., Hellmig, M., & Puelles, V. G. (2024). pyclustree: Visualizing cluster resolution optimization for biomedical data (0.3.1). Zenodo. https://doi.org/10.5281/zenodo.13987570
- clustree: Zappia, L., & Oshlack, A. (2018). Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience, 7(7), giy083.
[license]: https://github.com/complextissue/pyclustree/blob/main/LICENSE
[issue-tracker]: https://github.com/complextissue/pyclustree/issues
[changelog]: https://pyclustree.readthedocs.io/latest/changelog.html
[link-docs]: https://pyclustree.readthedocs.io
[link-pypi]: https://pypi.org/project/pyclustree