scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
13 of 75 committers (17.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (18.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Deep probabilistic analysis of single-cell and spatial omics data
Basic Info
- Host: GitHub
- Owner: scverse
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: http://scvi-tools.org/
- Size: 150 MB
Statistics
- Stars: 1,429
- Watchers: 26
- Forks: 402
- Open Issues: 34
- Releases: 89
Topics
Metadata Files
README.md
scvi-tools is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
Analysis of single-cell omics data
scvi-tools is composed of models that perform many analysis tasks across single-cell, multi, and spatial omics data:
- Dimensionality reduction
- Data integration
- Automated annotation
- Factor analysis
- Doublet detection
- Spatial deconvolution
- and more!
In the user guide, we provide an overview of each model. All model implementations have a high-level API that interacts with Scanpy and includes standard save/load functions, GPU acceleration, etc.
Rapid development of novel probabilistic models
scvi-tools contains the building blocks to develop and deploy novel probabilistic models. These building blocks are powered by popular probabilistic and machine learning frameworks such as PyTorch Lightning and Pyro. For an overview of how the scvi-tools package is structured, you may refer to the codebase overview page.
We recommend checking out the skeleton repository as a starting point for developing and deploying new models with scvi-tools.
Basic installation
For conda,
bash
conda install scvi-tools -c conda-forge
and for pip,
bash
pip install scvi-tools
Please be sure to install a version of PyTorch that is compatible with your GPU (if applicable).
Resources
- Tutorials, API reference, and installation guides are available in the documentation.
- For discussion of usage, check out our forum.
- Please use the issues to submit bug reports.
- If you'd like to contribute, check out our contributing guide.
- If you find a model useful for your research, please consider citing the corresponding publication.
Reference
If you use scvi-tools in your work, please cite
A Python library for probabilistic analysis of single-cell omics data
Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mariano Gabitto, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-López, Lior Pachter, Fabian J. Theis, Aaron Streets, Michael I. Jordan, Jeffrey Regier & Nir Yosef
Nature Biotechnology 2022 Feb 07. doi: 10.1038/s41587-021-01206-w.
along with the publication describing the model used.
You can cite the scverse publication as follows:
The scverse project provides a computational ecosystem for single-cell omics data analysis
Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis
Nature Biotechnology 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.
scvi-tools is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS.
If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science
Owner
- Name: scverse
- Login: scverse
- Kind: organization
- Website: https://scverse.org
- Twitter: scverse_team
- Repositories: 28
- Profile: https://github.com/scverse
Foundational tools for omics data in the life sciences
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| adamgayoso | a****o | 1,689 |
| galen xing | g****3@c****u | 449 |
| Martin Kim | 4****0 | 334 |
| Pierre Boyeau | p****u@g****m | 127 |
| Romain Lopez | r****z@b****u | 126 |
| Edouard360 | m****n@g****m | 114 |
| pre-commit-ci[bot] | 6****] | 100 |
| Jeffrey Regier | j****r | 94 |
| Ori Kronfeld | o****d@w****l | 94 |
| Justin Hong | j****2@b****u | 73 |
| talashuach | t****h@g****m | 53 |
| maxime | m****n@p****u | 45 |
| Vitalii Kleshchevnikov | v****v@s****k | 43 |
| Yining Liu | l****g@b****u | 40 |
| Valeh Valiollah Pour Amiri | 4****s | 33 |
| anazaret | a****t@g****m | 26 |
| Gabriel Misrachi | g****i@g****m | 25 |
| chenling antelope | c****e@g****m | 24 |
| Can Ergen | c****c@g****m | 22 |
| Valentine Svensson | v@n****e | 21 |
| jules-samaran | 4****n | 20 |
| mjayasur | m****r@b****u | 18 |
| github-actions[bot] | 4****] | 18 |
| Kathy Wu | k****u@b****u | 15 |
| njbernstein | n****n@g****m | 15 |
| Han Yuan | y****h@s****l | 6 |
| marianogabitto | m****o@g****m | 5 |
| Ethan Weinberger | e****r@g****m | 5 |
| Rohan Koodli | r****5@g****m | 4 |
| David Kelley | d****k@c****m | 4 |
| and 45 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 407
- Total pull requests: 1,827
- Average time to close issues: 5 months
- Average time to close pull requests: 12 days
- Total issue authors: 212
- Total pull request authors: 55
- Average comments per issue: 2.47
- Average comments per pull request: 1.0
- Merged pull requests: 1,498
- Bot issues: 1
- Bot pull requests: 187
Past Year
- Issues: 99
- Pull requests: 726
- Average time to close issues: 9 days
- Average time to close pull requests: 4 days
- Issue authors: 74
- Pull request authors: 25
- Average comments per issue: 1.87
- Average comments per pull request: 0.99
- Merged pull requests: 580
- Bot issues: 1
- Bot pull requests: 124
Top Authors
Issue Authors
- martinkim0 (73)
- adamgayoso (26)
- justjhong (11)
- scverse-bot (10)
- ori-kron-wis (8)
- vitkl (7)
- Hrovatin (5)
- shahrozeabbas (5)
- zacharyjxy2020 (5)
- yanwu2014 (4)
- canergen (4)
- Rafael-Silva-Oliveira (4)
- Zethson (4)
- Sirin24 (3)
- HelloWorldLTY (3)
Pull Request Authors
- meeseeksmachine (584)
- martinkim0 (512)
- ori-kron-wis (252)
- pre-commit-ci[bot] (134)
- canergen (66)
- github-actions[bot] (53)
- adamgayoso (50)
- justjhong (31)
- lordy5 (20)
- ethanweinberger (13)
- PierreBoyeau (8)
- LevyNat (7)
- lauradmartens (7)
- vitkl (6)
- mjayasur (4)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 54,278 last-month
- Total docker downloads: 2,965
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Total dependent packages: 43
(may contain duplicates) -
Total dependent repositories: 41
(may contain duplicates) - Total versions: 104
- Total maintainers: 5
pypi.org: scvi-tools
Deep probabilistic analysis of single-cell omics data.
- Documentation: https://scvi-tools.org
- License: BSD 3-Clause License Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Latest release: 1.3.3
published 7 months ago
Rankings
Maintainers (5)
proxy.golang.org: github.com/scverse/scvi-tools
- Documentation: https://pkg.go.dev/github.com/scverse/scvi-tools#section-documentation
- License: bsd-3-clause
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Latest release: v0.3.0
published almost 7 years ago
Rankings
Dependencies
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