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pyclustree

A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.

https://github.com/complextissue/pyclustree

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary

Keywords

clustree pyclustree scverse single-cell
Last synced: 6 months ago · JSON representation ·

Repository

A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.

Basic Info
Statistics
  • Stars: 8
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 5
Topics
clustree pyclustree scverse single-cell
Created over 1 year ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License Citation

README.md

pyclustree

Version License GitHub Actions Workflow Status Documentation Status Codecov Python Version Required DOI

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), however, while we aim to provide the same functionality, the API will differ between the implementations.

Getting started

Please refer to the documentation.

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.

There are several alternative options to install pyclustree:

  1. Install the latest release of pyclustree from PyPI:

bash pip install pyclustree

  1. 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.

Authors

@maltekuehl @harryhaller001

Unaffiliated with the creators of the R package clustree.

License

Please refer to the 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.

Owner

  • Name: Complex Tissue lab
  • Login: complextissue
  • Kind: organization
  • Location: Denmark

Research group led by Prof. Victor Puelles, PhD, at Aarhus University.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use pyclustree, please cite it as below. Please also cite the original clustree package."
authors:
    - family-names: "Kuehl"
      given-names: "Malte"
    - family-names: "Hellmig"
      given-names: "Malte"
    - family-names: "Puelles"
      given-names: "Victor G."
title: "pyclustree: Visualizing cluster resolution optimization for biomedical data"
version: 0.4.1
date-released: 2025-06-08
url: "https://zenodo.org/records/13987570"

GitHub Events

Total
  • Create event: 6
  • Issues event: 3
  • Release event: 3
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 17
  • Pull request review event: 3
  • Pull request review comment event: 6
  • Pull request event: 2
Last Year
  • Create event: 6
  • Issues event: 3
  • Release event: 3
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 17
  • Pull request review event: 3
  • Pull request review comment event: 6
  • Pull request event: 2

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 193 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
pypi.org: pyclustree

Visualize cluster assignments at different resolutions

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 193 Last month
Rankings
Dependent packages count: 10.3%
Average: 34.2%
Dependent repos count: 58.2%
Maintainers (1)
mkuehl
Last synced: 6 months ago