Package Health Score

57 / 100

security
Security review needed
popularity
Small
maintenance
Inactive
community
Active

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Popularity

Small

GitHub Stars: 1.21K
Forks: 344
Contributors: 70

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package scvi, we found that it has been starred 1,207 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Sep 16, 2020
Direct Vulnerabilities: 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

Inactive

Commit Frequency

Open Issues: 49
Open PR: 13
Last Release: 4 years ago
Last Commit: 17 days ago

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

An important project maintenance signal to consider for scvi is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

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: No
Code of Conduct: Yes
Contributors: 70
Funding: No

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

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Package

Python Versions Compatibility: >=3.6

Age: 6 years
Latest Release: 4 years ago
Dependencies: 13 Direct / 47 Total
Versions: 25
Maintainers: 5
Wheels: OS Independent

Readme

scVI - Single cell Variational Inference

scVI is a package for end-to-end analysis of single-cell omics data. The package is composed of several deep generative models for omics data analysis, namely:

scVI for analysis of single-cell RNA-seq data, as well as its improved differential expression framework
scANVI for cell annotation of scRNA-seq data using semi-labeled examples
totalVI for analysis of CITE-seq data
gimVI for imputation of missing genes in spatial transcriptomics from scRNA-seq data
AutoZI for assessing gene-specific levels of zero-inflation in scRNA-seq data
LDVAE for an interpretable linear factor model version of scVI

Tutorials and API reference are available in the documentation. Please use the issues here to discuss usage, or submit bug reports. If you'd like to contribute, please check out our contributing guide. If you find a model useful for your research, please consider citing the corresponding publication (linked above).

Package transition

scvi is transitioning to scvi-tools. If you're looking for scvi source code, please use the branch tags. scvi is still available via pypi and bioconda, but there will be no future releases past 0.6.8. An alpha-release of scvi-tools will be available shortly.

History

0.6.8 (2020-9-16)

scvi is now deprecated, please uninstall and install scvi-tools (available shortly)

0.6.7 (2020-8-05)

downgrade anndata>=0.7 and scanpy>=1.4.6 @galen
make loompy optional, raise sckmisc import error @adam
fix PBMCDataset download bug @galen
fix AnnDatasetFromAnnData _X in adata.obs bug @galen

0.6.6 (2020-7-08)

add tqdm to within cluster DE genes @adam
restore tqdm to use simple bar instead of ipywidget @adam
move to numpydoc for doctstrings @adam
update issues templates @adam
Poisson variable gene selection @valentine-svensson
BrainSmallDataset set defualt save_path_10X @gokcen-eraslan
train_size must be float between 0.0 and 1.0 @galen
bump dependency versions @galen
remove reproducibility notebook @galen
fix scanVI dataloading @pierre

0.6.5 (2020-5-10)

updates to totalVI posterior functions and notebooks @adam
update seurat v3 HVG selection now using skmisc loess @adam

0.6.4 (2020-4-14)

add back Python 3.6 support @adam
get_sample_scale() allows gene selection @valentine-svensson
bug fix to the dataset to anndata method with how cell measurements are stored @adam
fix requirements @adam

0.6.3 (2020-4-01)

bug in version for Louvian in setup.py @adam

0.6.2 (2020-4-01)

update highly variable gene selection to handle sparse matrices @adam
update DE docstrings @pierre
improve posterior save load to also handle subclasses @pierre
Create NB and ZINB distributions with torch and refactor code accordingly @pierre
typos in autozivae @achille
bug in csc sparse matrices in anndata data loader @adam

0.6.1 (2020-3-13)

handles gene and cell attributes with the same name @han-yuan
fixes anndata overwriting when loading @adam, @pierre
formatting in basic tutorial @adam

0.6.0 (2020-2-28)

updates on TotalVI and LDVAE @adam
fix documentation, compatibility and diverse bugs @adam, @pierre @romain
fix for external module on scanpy @galen

0.5.0 (2019-10-17)

do not automatically upper case genes @adam
AutoZI @oscar
Made the intro tutorial more user friendly @adam
Tests for LDVAE notebook @adam
black codebase @achille @gabriel @adam
fix compatibility issues with sklearn and numba @romain
fix Anndata @francesco-brundu
docstring, totalVI, totalVI notebook and CITE-seq data @adam
fix type @eduardo-beltrame
fixing installation guide @jeff
improved error message for dispersion @stephen-flemming

0.4.1 (2019-08-03)

docstring @achille
differential expression @oscar @pierre

0.4.0 (2019-07-25)

gimVI @achille
synthetic correlated datasets, fixed bug in marginal log likelihood @oscar
autotune, dataset enhancements @gabriel
documentation @jeff
more consistent posterior API, docstring, validation set @adam
fix anndataset @michael-raevsky
linearly decoded VAE @valentine-svensson
support for scanpy, fixed bugs, dataset enhancements @achille
fix filtering bug, synthetic correlated datasets, docstring, differential expression @pierre
better docstring @jamie-morton
classifier based on library size for doublet detection @david-kelley

0.3.0 (2019-05-03)

corrected notebook @jules
added UMAP and updated harmonization code @chenling @romain
support for batch indices in csvdataset @primoz-godec
speeding up likelihood computations @william-yang
better anndata interop @casey-greene
early stopping based on classifier accuracy @david-kelley

0.2.4 (2018-12-20)

updated to torch v1 @jules
added stress tests for harmonization @chenling
fixed autograd breaking @romain
make removal of empty cells more efficient @john-reid
switch to os.path.join @casey-greene

0.2.2 (2018-11-08)

added baselines and datasets for sMFISH imputation @jules
added harmonization content @chenling
fixing bugs on DE @romain

0.2.0 (2018-09-04)

annotation notebook @eddie
Memory footprint management @jeff
updated early stopping @max
docstring @james-webber

0.1.6 (2018-08-08)

MMD and adversarial inference wrapper @eddie
Documentation @jeff
smFISH data imputation @max

0.1.5 (2018-07-24)

Dataset additions @eddie
Documentation @yining
updated early stopping @max

0.1.3 (2018-06-22)

Notebook enhancement @yining
Semi-supervision @eddie

0.1.2 (2018-06-13)

First release on PyPi
Skeleton code & dependencies @jeff
Unit tests @max
PyTorch implementation of scVI @eddie @max
Dataset preprocessing @eddie @max @yining

0.1.0 (2017-09-05)

First scVI TensorFlow version @romain

scvi dependencies

anndata dataclasses h5py hyperopt matplotlib numpy pandas scanpy scikit-learn scikit-misc torch tqdm xlrd

FAQs

What is scvi?

Single-cell Variational Inference. Visit Snyk Advisor to see a full health score report for scvi, including popularity, security, maintenance & community analysis.

Is scvi popular?

The python package scvi receives a total of 504 weekly downloads. As such, scvi popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is scvi well maintained?

We found indications that scvi is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is scvi safe to use?

While scanning the latest version of scvi, 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 8 October-2024, at 02:46 (UTC).

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