View scArches on Snyk Open Source Advisor

Package Health Score

59 / 100

security
Security review needed
popularity
Limited
maintenance
Sustainable
community
Sustainable

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42

Popularity

Limited

GitHub Stars: 335
Forks: 51
Contributors: 30

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package scArches, we found that it has been starred 335 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Feb 29, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 2
H
4
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

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Maintenance

Sustainable

Commit Frequency

Open Issues: 46
Open PR: 7
Last Release: 9 months ago
Last Commit: 6 months ago

Further analysis of the maintenance status of scArches based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Sustainable.

We found that scArches demonstrates a positive version release cadence with at least one new version released in the past 12 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: No
Contributors: 30
Funding: No

With more than 10 contributors for the scArches repository, this is possibly a sign for a growing and inviting community.

We found a way for you to contribute to the project! Looks like scArches is missing a Code of Conduct.

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Package

Python Versions Compatibility: ==3.9.*

Age: 4 years
Latest Release: 9 months ago
Dependencies: 16 Direct / 120 Total
Versions: 28
Maintainers: 4
Wheels: OS Independent

Readme

.. raw:: html

Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data.

What is scArches?

scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations.

Usage and installation

See here _ for documentation and tutorials.

Support and contribute

If you have a question or new architecture or a model that could be integrated into our pipeline, you can post an issue __ or reach us by email _.

Reference

If scArches is helpful in your research, please consider citing the following paper _: ::

   @article{lotfollahi2021mapping,
     title={Mapping single-cell data to reference atlases by transfer learning},
     author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi,
     Matin and B{\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\v{Z}}iga and Gayoso,
     Adam and Yosef, Nir and Interlandi, Marta and others},
     journal={Nature Biotechnology},
     pages={1--10},
     year={2021},
     publisher={Nature Publishing Group}}

.. |PyPI| image:: https://img.shields.io/pypi/v/scarches.svg :target: https://pypi.org/project/scarches

.. |PyPIDownloads| image:: https://pepy.tech/badge/scarches :target: https://pepy.tech/project/scarches

.. |Docs| image:: https://readthedocs.org/projects/scarches/badge/?version=latest :target: https://scarches.readthedocs.io

scArches dependencies

anndata gdown h5py leidenalg matplotlib muon numpy pandas requests scanpy schpl scikit-learn scipy scvi-tools torch tqdm

FAQs

What is scArches?

Transfer learning with Architecture Surgery on Single-cell data. Visit Snyk Advisor to see a full health score report for scArches, including popularity, security, maintenance & community analysis.

Is scArches popular?

The python package scArches receives a total of 851 weekly downloads. As such, scArches popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is scArches well maintained?

We found indications that scArches maintenance is sustainable demonstrating some project activity. We saw a total of 30 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is scArches safe to use?

While scanning the latest version of scArches, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 25 November-2024, at 10:56 (UTC).

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scArches

Transfer learning with Architecture Surgery on Single-cell data For more information about how to use this package see README

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Readme

What is scArches?

Usage and installation

Support and contribute

Reference

scArches dependencies

FAQs

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Readme

What is scArches?

Usage and installation

Support and contribute

Reference

scArches dependencies

FAQs

What is scArches?

Is scArches popular?

Is scArches well maintained?

Is scArches safe to use?

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Source Code

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