View scanpy on Snyk Open Source Advisor

Package Health Score

93 / 100

security
No known security issues
popularity
Popular
maintenance
Healthy
community
Active

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Popularity

Popular

GitHub Stars: 1.74K
Forks: 569
Contributors: 140

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package scanpy, we found that it has been starred 1,742 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Apr 9, 2024
Direct Vulnerabilities: 0
C
0
H
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

Healthy

Commit Frequency

Open Issues: 493
Open PR: 59
Last Release: 10 days ago
Last Commit: 4 days ago

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

We found that scanpy demonstrates a positive version release cadence with at least one new version released in the past 3 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: 140
Funding: No

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

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Package

Python Versions Compatibility: >=3.9

Age: 7 years
Latest Release: 10 days ago
Dependencies: 5 Direct
Versions: 78
Maintainers: 3
Wheels: OS Independent

Not sure how to use scanpy?

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

theislab / trVAE / tests / monitor_beta.py View on Github

def create_data(data_dict):
    data_name = data_dict['name']
    source_keys = data_dict.get("source_conditions")
    target_keys = data_dict.get("target_conditions")
    cell_type_key = data_dict.get("cell_type_key", None)
    condition_key = data_dict.get('condition_key', 'condition')
    spec_cell_type = data_dict.get("spec_cell_types", None)[0]

    adata = sc.read(f"./data/{data_name}/{data_name}_normalized.h5ad")
    adata = adata[adata.obs[condition_key].isin(source_keys + target_keys)]

    if adata.shape[1] > 2000:
        sc.pp.highly_variable_genes(adata, n_top_genes=2000)
        adata = adata[:, adata.var['highly_variable']]

    train_adata, valid_adata = train_test_split(adata, 0.80)

    net_train_adata = train_adata.copy()[~((train_adata.obs[cell_type_key] == spec_cell_type) &
                                           (train_adata.obs[condition_key].isin(target_keys)))]
    net_valid_adata = valid_adata.copy()[~((valid_adata.obs[cell_type_key] == spec_cell_type) &
                                           (valid_adata.obs[condition_key].isin(target_keys)))]
    return adata, net_train_adata, net_valid_adata

View more ways to use scanpy

scanpy dependencies

joblib natsort patsy session-info tqdm

FAQs

What is scanpy?

Single-Cell Analysis in Python. Visit Snyk Advisor to see a full health score report for scanpy, including popularity, security, maintenance & community analysis.

Is scanpy popular?

The python package scanpy receives a total of 45,221 weekly downloads. As such, scanpy popularity was classified as a popular. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is scanpy well maintained?

We found that scanpy demonstrated a healthy version release cadence and project activity. It has a community of 140 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is scanpy safe to use?

The python package scanpy 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 18 April-2024, at 15:10 (UTC).

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scanpy

Single-Cell Analysis in Python. For more information about how to use this package see README

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Not sure how to use scanpy?

Scanpy – Single-Cell Analysis in Python

Citation

scanpy dependencies

FAQs

What is scanpy?

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Is scanpy well maintained?

Is scanpy safe to use?

Build a secure application checklist

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Fix identified vulnerabilities

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Package Health Score

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Direct Usage Popularity

Security and license risk for latest version

Commit Frequency

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Keep your project healthy

Check your requirements.txt

Snyk Vulnerability Scanner

Not sure how to use scanpy?

Scanpy – Single-Cell Analysis in Python

Citation

scanpy dependencies

FAQs

What is scanpy?

Is scanpy popular?

Is scanpy well maintained?

Is scanpy safe to use?

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Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

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