Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 16 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 19 committers (5.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Keywords from Contributors
Repository
RNA Velocity generalized through dynamical modeling
Basic Info
- Host: GitHub
- Owner: theislab
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://scvelo.org
- Size: 46.5 MB
Statistics
- Stars: 461
- Watchers: 12
- Forks: 109
- Open Issues: 72
- Releases: 5
Metadata Files
README.md
scVelo - RNA velocity generalized through dynamical modeling
scVelo is a scalable toolkit for RNA velocity analysis in single cells; RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics 1. scVelo collects different methods for inferring RNA velocity using an expectation-maximization framework 2, deep generative modeling 3, or metabolically labeled transcripts4.
scVelo's key applications
- estimate RNA velocity to study cellular dynamics.
- identify putative driver genes and regimes of regulatory changes.
- infer a latent time to reconstruct the temporal sequence of transcriptomic events.
- estimate reaction rates of transcription, splicing and degradation.
- use statistical tests, e.g., to detect different kinetics regimes.
Citing scVelo
If you include or rely on scVelo when publishing research, please adhere to the following citation guide:
EM and steady-state model
If you use the EM (dynamical) or steady-state model, cite
bibtex
@article{Bergen2020,
title = {Generalizing RNA velocity to transient cell states through dynamical modeling},
volume = {38},
ISSN = {1546-1696},
url = {http://dx.doi.org/10.1038/s41587-020-0591-3},
DOI = {10.1038/s41587-020-0591-3},
number = {12},
journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
author = {Bergen, Volker and Lange, Marius and Peidli, Stefan and Wolf, F. Alexander and Theis, Fabian J.},
year = {2020},
month = aug,
pages = {1408–1414}
}
RNA velocity inference through metabolic labeling information
If you use the implemented method for estimating RNA velocity from metabolic labeling information, cite
bibtex
@article{Weiler2024,
author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe'er, Dana and Theis, Fabian},
publisher = {Springer Science and Business Media LLC},
url = {http://dx.doi.org/10.1038/s41592-024-02303-9},
doi = {10.1038/s41592-024-02303-9},
issn = {1548-7105},
journal = {Nature Methods},
month = jun,
number = {7},
pages = {1196--1205},
title = {CellRank 2: unified fate mapping in multiview single-cell data},
volume = {21},
year = {2024},
}
Support
Found a bug or would like to see a feature implemented? Feel free to submit an issue. Have a question or would like to start a new discussion? Head over to GitHub discussions. Your help to improve scVelo is highly appreciated. For further information visit scvelo.org.
Owner
- Name: Theis Lab
- Login: theislab
- Kind: organization
- Email: icb.office@helmholtz-muenchen.de
- Location: Munich
- Website: https://www.helmholtz-muenchen.de/icb/
- Repositories: 213
- Profile: https://github.com/theislab
Institute of Computational Biology
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 36
- Watch event: 39
- Issue comment event: 48
- Pull request event: 5
- Fork event: 7
Last Year
- Create event: 1
- Release event: 1
- Issues event: 36
- Watch event: 39
- Issue comment event: 48
- Pull request event: 5
- Fork event: 7
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| VBergen | v****n@t****e | 922 |
| Philipp Weiler | w****p@g****m | 82 |
| stefanpeidli | s****i@g****m | 38 |
| Volker Bergen | 3****n | 22 |
| Philipp A | f****p@w****e | 20 |
| Marius Lange | m****e@t****e | 10 |
| Michal Klein | m****n@t****m | 9 |
| michalk8 | m****n@p****m | 3 |
| Ramirez,Dr.,Fidel (RES I+R) BIP-DE-B | f****z@b****m | 3 |
| michalk8 | 4****8 | 3 |
| Francesco G. Brundu | f****u@g****m | 3 |
| Adam Gayoso | a****o | 2 |
| Miles Smith | 3****h | 2 |
| VolkerBergen | e****l@v****e | 1 |
| moloch | 1****0 | 1 |
| Gökçen Eraslan | g****n@g****m | 1 |
| VolkerBergen | V****7 | 1 |
| Johanna Schneeberger | 7****e | 1 |
| Saksham Malhotra | s****6@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 265
- Total pull requests: 69
- Average time to close issues: about 2 months
- Average time to close pull requests: 14 days
- Total issue authors: 168
- Total pull request authors: 18
- Average comments per issue: 2.32
- Average comments per pull request: 0.45
- Merged pull requests: 59
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 30
- Pull requests: 11
- Average time to close issues: 14 days
- Average time to close pull requests: about 2 hours
- Issue authors: 23
- Pull request authors: 5
- Average comments per issue: 0.7
- Average comments per pull request: 0.09
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- WeilerP (57)
- jwalewski (7)
- danli349 (4)
- zhouzhendiao (4)
- mimisikai (4)
- denvercal1234GitHub (4)
- Flu09 (3)
- vasikara17 (3)
- chen-peng-1874 (3)
- dawe (3)
- reneemoerkens (3)
- mayurdoke6 (2)
- smallfishcui (2)
- akhst7 (2)
- DaianeH (2)
Pull Request Authors
- WeilerP (55)
- michalk8 (4)
- Oisin-M (4)
- jwalewski (3)
- h4rvey-g (2)
- IsaacUtah1379 (2)
- VolkerBergen (2)
- Abelgurung (2)
- adamgayoso (2)
- Zethson (2)
- milescsmith (1)
- rwiegan (1)
- idriskb (1)
- patjiang (1)
- martinkim0 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 9,288 last-month
- Total docker downloads: 1,663
- Total dependent packages: 28
- Total dependent repositories: 34
- Total versions: 34
- Total maintainers: 2
pypi.org: scvelo
RNA velocity generalized through dynamical modeling
- Documentation: https://scvelo.readthedocs.io/
- License: BSD 3-Clause License Copyright (c) 2018, Theis Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 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. * 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: 0.3.3
published over 1 year ago
Rankings
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- mstachniuk/ci-skip master composite
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- loompy >=2.0.12
- matplotlib >=3.3.0
- numba >=0.41.0
- numpy >=1.17
- pandas >=0.23, !=1.4.0
- scanpy >=1.5
- scikit-learn >=0.21.2, <1.2.0
- scipy >=1.4.1
- umap-learn >=0.3.10
- actions/checkout v2 composite
- actions/setup-python v2 composite