infercnvpy

v0.5.0

Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable. For more information about how to use this package see README

Latest version published 6 months ago

License: BSD-3-Clause

PyPI

GitHub

Package Health Score

70 / 100

security
No known security issues
popularity
Limited
maintenance
Sustainable
community
Active

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Popularity

Limited

GitHub Stars: 140
Forks: 27
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package infercnvpy, we found that it has been starred 140 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Jun 26, 2024
Direct Vulnerabilities: 0
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0
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Indirect Vulnerabilities: 0
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License Risk: 0
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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: 15
Open PR: 3
Last Release: 6 months ago
Last Commit: 5 months ago

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

We found that infercnvpy 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

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: No
Contributors: 20
Funding: No

With more than 10 contributors for the infercnvpy 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 infercnvpy is missing a Code of Conduct.

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Package

Python Versions Compatibility: >=3.10

Age: 4 years
Latest Release: 6 months ago
Dependencies: 6 Direct
Versions: 12
Maintainers: 0
Wheels: OS Independent

Readme

infercnvpy: Scanpy plugin to infer copy number variation (CNV) from single-cell transcriptomics data

Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable.

The main result of infercnv

WARNING:

This package is still experimental. The results have not been validated, except in that they look similar, but not identical, to the results of InferCNV.

We are happy about feedback and welcome contributions!

Getting started

Please refer to the documentation. In particular, the

API 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 infercnvpy:

Install the latest release of infercnvpy from PyPI _:

pip install infercnvpy

Install the latest development version:

pip install git+https://github.com/icbi-lab/infercnvpy.git@main

To (optionally) run the copyKAT algorithm, you need a working R installation and the copykat package installed. Usually, if R is in your PATH, rpy2 automatically detects your R installation. If you get an error message while importing infercnvpy, try setting the R_HOME environment variable before importing infercnvpy:

import os

os.environ["R_HOME"] = "/usr/lib/R"
import infercnvpy

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

n/a

infercnvpy dependencies

ipython leidenalg pyreadr pytest-benchmark pytoml session-info

FAQs

What is infercnvpy?

Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data... Visit Snyk Advisor to see a full health score report for infercnvpy, including popularity, security, maintenance & community analysis.

Is infercnvpy popular?

The python package infercnvpy receives a total of 424 weekly downloads. As such, infercnvpy popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is infercnvpy well maintained?

We found indications that infercnvpy maintenance is sustainable demonstrating some project activity. We saw a total of 20 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is infercnvpy safe to use?

The python package infercnvpy was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 19 December-2024, at 16:50 (UTC).

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