pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

https://github.com/pinellolab/pyrovelocity

Science Score: 57.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary

Keywords

cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics

Last synced: 4 months ago · JSON representation ·

Repository

𝒫robabilistic modeling of RNA velocity ⬱

Basic Info

Host: GitHub
Owner: pinellolab
License: agpl-3.0
Language: Python
Default Branch: main
Homepage: https://docs.pyrovelocity.net
Size: 25.7 MB

Statistics

Stars: 47
Watchers: 6
Forks: 5
Open Issues: 32
Releases: 47

Topics

Created over 3 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codeowners Security

README.md

Pyro-Velocity

𝒫robabilistic modeling of RNA velocity ⬱ | | | | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------ | | CI/CD | [![CID][cid-badge]][cid-link] [![codecov][codecov-badge]][codecov-link] [![pre-commit.ci status][precommit-badge]][precommit-link] | | Docs | [![Cloudflare Pages][cloudflare-badge]][cloudflare-link] [![Preprint][preprint-badge]][preprint-link] | | Package | [![PyPI - Version][pypi-badge]][pypi-link] [![Conda-forge badge][conda-forge-badge]][anaconda-link] [![Docker image][docker-badge]][docker-link] | | Meta | [![pyro-ppl-badge]][pyro-ppl-link] [![flyte-badge]][flyte-link] [![hydra-zen-badge]][hydra-zen-link] [![scvi-tools-badge]][scvi-tools-link] | | | [![bear-badge]][bear-link] [![black-badge]][black-link] [![License][license-badge]][license-link] [![Tuple][tuple-badge]][tuple-link] |

Pyro-Velocity is a library for probabilistic inference in minimal models approximating gene expression dynamics from, possibly multimodal, single-cell sequencing data. It provides posterior estimates of gene expression parameters, predictive estimates of gene expression states, and local estimates of cell state transition probabilities. It can be used as a component in frameworks that attempt to retain the ability to propagate uncertainty in predicting: distributions over cell fates from subpopulations of cell states, response to cell state perturbations, or candidate genes or gene modules that correlate with determination of specific cell fates.

Documentation 📒

Please see the Documentation.

Changelog 🔀

Changes for each release are listed in the Changelog.

Contributing ✨

Please review the Contributing Guide for instructions on setting up a development environment and submitting pull requests.

Community 🏘

If you would like to apply Pyro-Velocity in your research, have an idea for a new feature, have a problem using the library, or just want to chat, please feel free to start a discussion.

If you have a feature request or issue using Pyro-Velocity that may require making changes to the contents of this repository, please file an issue containing

a GitHub permananent link to the location in the repository you think is causing a problem or will require changes, and
provide a minimal reproducible example of the problem or proposed improvement.

We are always interested in discussions and issues that can help to improve the Documentation.

License ⚖️

AGPL

Owner

Name: Pinello Lab
Login: pinellolab
Kind: organization
Email: lpinello@mgh.harvard.edu
Location: Boston

Website: pinellolab.org
Repositories: 22
Profile: https://github.com/pinellolab

Massachusetts General Hospital/ Harvard Medical School

Citation (CITATION.bib)

@ARTICLE{Qin2022-ls,
  title    = "{Pyro-Velocity}: Probabilistic {RNA} Velocity inference from
              single-cell data",
  author   = "Qin, Qian and Bingham, Eli and La Manno, Gioele and Langenau,
              David M and Pinello, Luca",
  journal  = "bioRxiv",
  pages    = "2022.09.12.507691",
  month    =  Sep,
  year     =  2022,
  language = "en",
  doi      = "10.1101/2022.09.12.507691"
}

GitHub Events

Total

Create event: 30
Release event: 6
Issues event: 28
Watch event: 6
Delete event: 8
Issue comment event: 5
Push event: 413
Pull request review event: 1
Pull request event: 20

Last Year

Create event: 30
Release event: 6
Issues event: 28
Watch event: 6
Delete event: 8
Issue comment event: 5
Push event: 413
Pull request review event: 1
Pull request event: 20

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 50
Total Committers: 4
Avg Commits per committer: 12.5
Development Distribution Score (DDS): 0.48

Top Committers

Name	Email	Commits
Cameron Smith	c**h@g**m	26
Qian Alvin Qin	q**n@u**m	10
qinqian	q**d@g**m	9
Luca Pinello	l**o@g**m	5

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 143
Total pull requests: 398
Average time to close issues: 15 days
Average time to close pull requests: 14 days
Total issue authors: 6
Total pull request authors: 8
Average comments per issue: 0.1
Average comments per pull request: 0.84
Merged pull requests: 244
Bot issues: 1
Bot pull requests: 210

Past Year

Issues: 44
Pull requests: 89
Average time to close issues: 20 days
Average time to close pull requests: 7 days
Issue authors: 3
Pull request authors: 4
Average comments per issue: 0.16
Average comments per pull request: 0.18
Merged pull requests: 52
Bot issues: 0
Bot pull requests: 50

View more stats

Top Authors

Issue Authors

cameronraysmith (122)
lijc0804 (3)
qinqian (1)
AlexanderAivazidis (1)
renovate[bot] (1)
edawu11 (1)

Pull Request Authors

cameronraysmith (191)
renovate[bot] (133)
dependabot[bot] (117)
qinqian (22)
lijc0804 (12)
pre-commit-ci[bot] (6)
AlexanderAivazidis (4)
mattlevine22 (2)

Top Labels

Issue Labels

enhancement (55) testing (13) dependencies (11) documentation (10) bug (10) refactoring (8) ci (7) build (6) data (6) github_actions (1) external (1)

Pull Request Labels

dependencies (255) python (164) enhancement (124) documentation (27) skip-ci (18) ci (17) github_actions (17) testing (17) bug (13) build (12) execute-workflow (12) refactoring (11) data (8) dev-mode (6) performance (4) work-in-progress (2) question (2) build-images (2) star (1) docs-preview (1)

Packages

Total packages: 1
Total downloads:
- pypi 67 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 46
Total maintainers: 3

pypi.org: pyrovelocity

A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro.

Homepage: https://docs.pyrovelocity.net
Documentation: https://docs.pyrovelocity.net
License: AGPL-3.0-only
Latest release: 0.4.5
published 9 months ago

Versions: 46
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 67 Last month

Rankings

Dependent packages count: 6.6%

Stargazers count: 13.9%

Average: 19.4%

Forks count: 19.6%

Downloads: 26.3%

Dependent repos count: 30.6%

Maintainers (3)

lucapinello cameronraysmith qianqin1.1

Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi

furo ==2022.9.29
myst_parser ==0.18.1
nbsphinx ==0.8.9
sphinx ==5.2.3
sphinx-click ==4.3.0
sphinx_autodoc_typehints ==1.19.4
sphinx_copybutton ==0.5.0

requirements_dev.txt pypi

Sphinx ==1.8.5 development
bump2version ==0.5.11 development
coverage ==4.5.4 development
flake8 ==3.7.8 development
pip ==19.2.3 development
tox ==3.14.0 development
twine ==1.14.0 development
watchdog ==0.9.0 development
wheel ==0.33.6 development