cellbrowser

v1.2.8

UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger. For more information about how to use this package see README

Latest version published 4 months ago

License: GPL-3.0

PyPI

GitHub

Package Health Score

78 / 100

security
No known security issues
popularity
Small
maintenance
Sustainable
community
Active

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Popularity

Small

GitHub Stars: 105
Forks: 42
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package cellbrowser, we found that it has been starred 105 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Jul 9, 2024
Direct Vulnerabilities: 0
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0
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0
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0
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Indirect Vulnerabilities: 0
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0
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0
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License Risk: 1
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

GPL-3.0

Non-Permissive License

We noticed that this project uses a license which requires less permissive conditions such as disclosing the source code, stating changes or redistributing the source under the same license. It is advised to further consult the license terms before use.

Security Policy

We found a way for you to contribute to the project! Looks like cellbrowser is missing a security policy.

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Maintenance

Sustainable

Commit Frequency

No Recent Commits

Open Issues: 28
Open PR: 0
Last Release: 4 months ago
Last Commit: 2 years ago

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

We found that cellbrowser 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: 20
Funding: No

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

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Package

Python Versions Compatibility: >=2.5

Age: 6 years
Latest Release: 4 months ago
Dependencies: N/A
Versions: 162
Maintainers: 2
Wheels: No

Not sure how to use cellbrowser?

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

maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github

# create a mapping from symbol -> gene locations
        if "/" in geneType:
            defGenes = geneType.split("/")[1]
        elif genome=="hg38":
            defGenes = "gencode24"
        elif genome=="hg19":
            defGenes = "gencode19"
        elif genome=="mm10":
            defGenes = "gencode-m13"
        else:
            errAbort("Unclear how to map symbols to genome for db %s. Please adapt cellbrowser.py" % genome)

        logging.info("Using %s to map symbols to genome" % defGenes)

        geneToSym = cellbrowser.readGeneSymbols({'geneIdType':defGenes})
        geneLocsId = cellbrowser.parseGeneLocs(defGenes)
        geneLocs = {}
        for geneId, locs in iterItems(geneLocsId):
            sym = geneToSym[geneId]
            geneLocs[sym] = locs
    else:
        geneToSym = cellbrowser.readGeneSymbols({'geneIdType':geneType})
        geneLocs = cellbrowser.parseGeneLocs(geneType)

    matOfh = open(outMatrixFname, "w")
    clustOfh = open(clusterFname, "w")

    mr = cellbrowser.MatrixTsvReader()
    mr.open(inMatrixFname)
    matType, cellNames = mr.matType, mr.sampleNames

    cellIds = range(0, len(cellNames))

View more ways to use cellbrowser

The UCSC Cell Browser is an interactive browser for single cell data, like mRNA or ATAC-seq data. You can display dimensionality reductions, navigate them with the mouse or the cursor keys, select cells, color by genes or meta annotations and make many other changes. The main site runs at https://cells.ucsc.edu, but using this package you can also convert data yourself and build a Cell Browser HTML directory that can be served through any University or any other webserver for static webpages. You can try the Cell Browser at https://cells.ucsc.edu or read about how to convert data with this package on https://cellbrowser.rtfd.org.

We strongly recommend that to use Python3, but we make an effort to remain compatible with Python2.

FAQs

What is cellbrowser?

UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, ... Visit Snyk Advisor to see a full health score report for cellbrowser, including popularity, security, maintenance & community analysis.

Is cellbrowser popular?

The python package cellbrowser receives a total of 2,172 weekly downloads. As such, cellbrowser popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is cellbrowser well maintained?

We found indications that cellbrowser 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 cellbrowser safe to use?

The python package cellbrowser 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 8 November-2024, at 09:18 (UTC).

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