View pyopenms on Snyk Open Source Advisor

Package Health Score

79 / 100

security
No known security issues
popularity
Small
maintenance
Sustainable
community
Active

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Popularity

Small

GitHub Stars: 455
Forks: 306
Contributors: 110

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package pyopenms, we found that it has been starred 455 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Oct 13, 2023
Direct Vulnerabilities: 0
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0
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0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
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: 588
Open PR: 46
Last Release: 6 months ago
Last Commit: 7 days ago

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

We found that pyopenms 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: Yes
Contributors: 110
Funding: Yes

A good and healthy external contribution signal for pyopenms project, which invites more than one hundred open source maintainers to collaborate on the repository.

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Package

Python Versions Compatibility: Unspecified

Age: 11 years
Latest Release: 6 months ago
Dependencies: 3 Direct
Versions: 17
Maintainers: 2
Wheels: Linux, macOS, Windows

Not sure how to use pyopenms?

To help you get started, we've collected the most common ways that pyopenms is being used within popular public projects.

OpenMS / OpenMS / src / pyOpenMS / pyTOPP / OpenSwathRTNormalizer.py View on Github

# set the correct rt use values
    scoring_params = pyopenms.MRMFeatureFinderScoring().getDefaults();
    scoring_params.setValue("Scores:use_rt_score",'false', '')
    featurefinder.setParameters(scoring_params);
    featurefinder.pickExperiment(chromatograms, output, targeted, trafo, empty_swath)

    # get the pairs
    pairs=[]
    simple_find_best_feature(output, pairs, targeted)
    pairs_corrected = pyopenms.MRMRTNormalizer().rm_outliers( pairs, 0.95, 0.6) 
    pairs_corrected = [ list(p) for p in pairs_corrected] 

    # // store transformation, using a linear model as default
    trafo_out = pyopenms.TransformationDescription()
    trafo_out.setDataPoints(pairs_corrected);
    model_params = pyopenms.Param()
    model_params.setValue("symmetric_regression", 'false', '');
    model_type = "linear";
    trafo_out.fitModel(model_type, model_params);
    return trafo_out

View more ways to use pyopenms

This package contains Python bindings for a large part of the OpenMS library for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).

You can install pyopenms using:

pip install pyopenms

Please see for more information.

pyopenms dependencies

matplotlib numpy pandas

FAQs

What is pyopenms?

Python wrapper for C++ LC-MS library OpenMS. Visit Snyk Advisor to see a full health score report for pyopenms, including popularity, security, maintenance & community analysis.

Is pyopenms popular?

The python package pyopenms receives a total of 4,559 weekly downloads. As such, pyopenms popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is pyopenms well maintained?

We found indications that pyopenms maintenance is sustainable demonstrating some project activity. We saw a total of 110 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is pyopenms safe to use?

The python package pyopenms 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 April-2024, at 23:32 (UTC).

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pyopenms

Python wrapper for C++ LC-MS library OpenMS For more information about how to use this package see README

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pyopenms dependencies

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What is pyopenms?

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Commit Frequency

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Not sure how to use pyopenms?

pyopenms dependencies

FAQs

What is pyopenms?

Is pyopenms popular?

Is pyopenms well maintained?

Is pyopenms safe to use?

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Source Code

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