spatialleiden

Implementation of multiplex Leiden for analysis of spatial omics data

https://github.com/hidihlabs/spatialleiden

Science Score: 57.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
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Academic publication links
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Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary

Last synced: 7 months ago · JSON representation ·

Repository

Implementation of multiplex Leiden for analysis of spatial omics data

Basic Info

Host: GitHub
Owner: HiDiHlabs
License: mit
Language: Python
Default Branch: main
Homepage: https://spatialleiden.readthedocs.io
Size: 80.1 KB

Statistics

Stars: 10
Watchers: 5
Forks: 0
Open Issues: 4
Releases: 3

Created almost 2 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

SpatialLeiden

SpatialLeiden is an implementation of Multiplex Leiden clustering that can be used to cluster spatially resolved omics data.

SpatialLeiden integrates with the scverse by leveraging anndata but can also be used independently.

Installation

spatialleiden is available on PyPI and bioconda.

```sh

PyPI

pip install spatialleiden ```

```sh

or conda

conda install bioconda::spatialleiden ```

For detailed installation instructions please refer to the documentation.

Documentation

For documentation of the package please refer to the ReadTheDocs page.

Citations

If you are using spatialleiden for your research please cite

Müller-Bötticher, N., Sahay, S., Eils, R., & Ishaque, N. (2025). SpatialLeiden: spatially aware Leiden clustering. Genome Biology, 26(1), 24. https://doi.org/10.1186/s13059-025-03489-7

@article{spatialleiden2025, author = {Müller-Bötticher, Niklas and Sahay, Shashwat and Eils, Roland and Ishaque, Naveed}, title = {SpatialLeiden: spatially aware Leiden clustering}, journal = {Genome Biology}, year = {2025}, month = {Feb}, day = {07}, volume = {26}, number = {1}, pages = {24}, doi = {10.1186/s13059-025-03489-7}, url = {https://doi.org/10.1186/s13059-025-03489-7} }

Versioning

This project follows the SemVer guidelines for versioning.

License

This project is licensed under the MIT License - for details please refer to the LICENSE file.

Owner

Name: HiDiH - Hub for Innovations in Digital Health
Login: HiDiHlabs
Kind: organization
Email: info@hidih.org
Location: Berlin, Germany

Website: https://www.hidih.org/
Twitter: HiDiHlabs
Repositories: 9
Profile: https://github.com/HiDiHlabs

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite the article from preferred-citation."
authors:
  - family-names: "Müller-Bötticher"
    given-names: Niklas
    orcid: "https://orcid.org/0000-0001-5103-7282"
  - family-names: Sahay
    given-names: Shashwat
    orcid: "https://orcid.org/0000-0002-8533-6149"
title: spatialleiden
url: "https://github.com/HiDiHlabs/SpatialLeiden"
date-released: '2024-05-30'
preferred-citation:
  type: article
  authors:
    - family-names: "Müller-Bötticher"
      given-names: Niklas
      orcid: "https://orcid.org/0000-0001-5103-7282"
    - family-names: Sahay
      given-names: Shashwat
      orcid: "https://orcid.org/0000-0002-8533-6149"
    - family-names: Eils
      given-names: Roland
      orcid: "https://orcid.org/0000-0002-0034-4036"
    - family-names: Ishaque
      given-names: Naveed
      orcid: "https://orcid.org/0000-0002-8426-901X"
  title: "SpatialLeiden: spatially aware Leiden clustering"
  doi: 10.1186/s13059-025-03489-7
  url: https://doi.org/10.1186/s13059-025-03489-7
  year: 2025
  journal: Genome Biology
  volume: 26
  issue: 1
  pages: 24

GitHub Events

Total

Create event: 2
Release event: 1
Issues event: 3
Watch event: 5
Delete event: 1
Issue comment event: 5
Push event: 33
Pull request review event: 1
Pull request event: 15

Last Year

Create event: 2
Release event: 1
Issues event: 3
Watch event: 5
Delete event: 1
Issue comment event: 5
Push event: 33
Pull request review event: 1
Pull request event: 15

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 1
Total pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: 7 days
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 3

Past Year

Issues: 1
Pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: 7 days
Issue authors: 1
Pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 3

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Top Authors

Issue Authors

niklasmueboe (2)
srivarra (1)

Pull Request Authors

niklasmueboe (5)
pre-commit-ci[bot] (3)

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 35 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3
Total maintainers: 1

pypi.org: spatialleiden

Implementation of multiplex Leiden for analysis of (multimodal) spatial omics data.

Homepage: https://github.com/HiDiHlabs/SpatialLeiden
Documentation: https://spatialleiden.readthedocs.io
License: mit
Latest release: 0.3.0
published 9 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 35 Last month

Rankings

Dependent packages count: 10.4%

Average: 34.6%

Dependent repos count: 58.8%

Maintainers (1)

niklasmueboe