https://github.com/theislab/cellrank

CellRank: dynamics from multi-view single-cell data

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 8 DOI reference(s) in README
✓
Academic publication links
Links to: nature.com
✓
Committers with academic emails
3 of 16 committers (18.8%) from academic institutions
✓
Institutional organization owner
Organization theislab has institutional domain (www.helmholtz-muenchen.de)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.8%) to scientific vocabulary

Keywords

bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation

Keywords from Contributors

anndata scanpy scverse transcriptomics visualize-data fitting probability statistical-analysis cite-seq scrna-seq

Last synced: 5 months ago · JSON representation

Repository

CellRank: dynamics from multi-view single-cell data

Basic Info

Host: GitHub
Owner: theislab
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://cellrank.org
Size: 95 MB

Statistics

Stars: 393
Watchers: 8
Forks: 50
Open Issues: 24
Releases: 6

Topics

Created almost 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License

README.rst

|PyPI| |Downloads| |CI| |Docs| |Codecov| |Discourse|

CellRank 2: Unified fate mapping in multiview single-cell data
==============================================================
.. image:: docs/_static/img/light_mode_overview.png#gh-light-mode-only
    :width: 600px
    :align: center
    :class: only-light

.. image:: docs/_static/img/dark_mode_overview.png#gh-dark-mode-only
    :width: 600px
    :align: center

**CellRank** is a modular framework to study cellular dynamics based on Markov state modeling of
multi-view single-cell data. See our `documentation`_, and the `CellRank 1`_ and `CellRank 2 manuscript`_ to learn more.

.. important::
    Please refer to `our citation guide `_ to cite our software correctly.

CellRank scales to large cell numbers, is fully compatible with the `scverse`_ ecosystem, and easy to use.
In the backend, it is powered by `pyGPCCA`_ (`Reuter et al. (2018)`_). Feel
free to open an `issue`_ if you encounter a bug, need our help or just want to make a comment/suggestion.

CellRank's key applications
---------------------------
- Estimate differentiation direction based on a varied number of biological priors, including RNA velocity
  (`La Manno et al. (2018)`_, `Bergen et al. (2020)`_), any pseudotime or developmental potential,
  experimental time points, metabolic labels, and more.
- Compute initial, terminal and intermediate macrostates.
- Infer fate probabilities and driver genes.
- Visualize and cluster gene expression trends.
- ... and much more, check out our `documentation`_.

.. |PyPI| image:: https://img.shields.io/pypi/v/cellrank.svg
    :target: https://pypi.org/project/cellrank
    :alt: PyPI

.. |Downloads| image:: https://static.pepy.tech/badge/cellrank
    :target: https://pepy.tech/project/cellrank
    :alt: Downloads

.. |Discourse| image:: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org
    :target: https://discourse.scverse.org/c/ecosystem/cellrank/
    :alt: Discourse

.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/cellrank/test.yml?branch=main
    :target: https://github.com/theislab/cellrank/actions
    :alt: CI

.. |Docs|  image:: https://img.shields.io/readthedocs/cellrank
    :target: https://cellrank.readthedocs.io/
    :alt: Documentation

.. |Codecov| image:: https://codecov.io/gh/theislab/cellrank/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/theislab/cellrank
    :alt: Coverage


.. _La Manno et al. (2018): https://doi.org/10.1038/s41586-018-0414-6
.. _Bergen et al. (2020): https://doi.org/10.1038/s41587-020-0591-3
.. _Reuter et al. (2018): https://doi.org/10.1021/acs.jctc.8b00079

.. _scverse: https://scverse.org/
.. _pyGPCCA: https://github.com/msmdev/pyGPCCA

.. _CellRank 1: https://www.nature.com/articles/s41592-021-01346-6
.. _CellRank 2 manuscript: https://doi.org/10.1038/s41592-024-02303-9
.. _documentation: https://cellrank.org

.. _issue: https://github.com/theislab/cellrank/issues/new/choose

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: 5
Release event: 2
Issues event: 51
Watch event: 41
Delete event: 2
Issue comment event: 61
Push event: 13
Pull request event: 14
Fork event: 2

Last Year

Create event: 5
Release event: 2
Issues event: 51
Watch event: 41
Delete event: 2
Issue comment event: 61
Push event: 13
Pull request event: 14
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 1,942
Total Committers: 16
Avg Commits per committer: 121.375
Development Distribution Score (DDS): 0.498

Past Year

Commits: 103
Committers: 8
Avg Commits per committer: 12.875
Development Distribution Score (DDS): 0.35

Top Committers

Name	Email	Commits
michalk8	m**n@p**m	974
Marius Lange	m**e@t**e	383
Michal Klein	m**n@t**m	276
michalk8	4****8	265
Marius1311	M****1	10
Philipp Weiler	w**p@g**m	8
Philipp Weiler	p**r@t**e	8
Marius Lange	m**e@t**e	6
WeilerP	W****P	5
soerenab	3****b	1
Giovanni Palla	2****p	1
Lukas Heumos	l**s@p**t	1
Oisin-M	6****M	1
Robert Schauner	r**6@c**u	1
pre-commit-ci[bot]	6****]	1
bfurtwa	b**r@w**e	1

Committer Domains (Top 20 + Academic)

tum.de: 2 case.edu: 1 posteo.net: 1 tngtech.com: 1 t-online.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 225
Total pull requests: 116
Average time to close issues: about 2 months
Average time to close pull requests: 11 days
Total issue authors: 129
Total pull request authors: 13
Average comments per issue: 2.8
Average comments per pull request: 1.66
Merged pull requests: 98
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 36
Pull requests: 20
Average time to close issues: 13 days
Average time to close pull requests: 2 days
Issue authors: 26
Pull request authors: 4
Average comments per issue: 0.97
Average comments per pull request: 1.3
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Marius1311 (26)
WeilerP (22)
michalk8 (13)
Zethson (6)
JenniferWUSTL (5)
hyjforesight (4)
liuyang218622 (3)
mainharryHR (3)
MUCDK (3)
BW15061999 (2)
wolfQK (2)
hl-xue (2)
JuliaChristiaanse (2)
jwalewski (2)
denvercal1234GitHub (2)

Pull Request Authors

michalk8 (43)
WeilerP (40)
Marius1311 (15)
MUCDK (3)
maximevtush (2)
afuetterer (2)
soerenab (2)
Abelgurung (2)
Zethson (2)
mxposed (2)
omahs (1)
bfurtwa (1)
giovp (1)

Top Labels

Issue Labels

question (89) bug (86) enhancement (34) documentation (6) doc (3)

Pull Request Labels

enhancement (10) bugfix (10) doc (6) bug (5) draft (4) misc (4) feature (3) ignore-towncrier (3) documentation (3) installation (1) deprecation (1)

Packages

Total packages: 1
Total downloads:
- pypi 2,911 last-month
Total docker downloads: 166

Total dependent packages: 5
Total dependent repositories: 5
Total versions: 35
Total maintainers: 3

pypi.org: cellrank

CellRank: dynamics from multi-view single-cell data

Homepage: https://github.com/theislab/cellrank
Documentation: https://cellrank.readthedocs.io
License: bsd-3-clause
Latest release: 2.0.7
published 11 months ago

Versions: 35
Dependent Packages: 5
Dependent Repositories: 5
Downloads: 2,911 Last month
Docker Downloads: 166

Rankings

Dependent packages count: 1.6%

Docker downloads count: 3.2%

Stargazers count: 3.9%

Average: 4.7%

Downloads: 6.1%

Dependent repos count: 6.6%

Forks count: 6.7%

Maintainers (3)

michalk8 s1nth0ra5 marius1311

Last synced: 6 months ago

Dependencies

.github/workflows/deployment.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
everlytic/branch-merge 1.1.2 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/news.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
stefanzweifel/git-auto-commit-action v4 composite

.github/workflows/release.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
benc-uk/workflow-dispatch v1 composite
stefanzweifel/git-auto-commit-action v4 composite

.github/workflows/test.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite
benc-uk/workflow-dispatch v1 composite
peter-evans/repository-dispatch v1 composite

docs/requirements.txt pypi

furo >=2022.06.04.1
ipywidgets *
jinja2 >=3.0.3
nbsphinx >=0.8,<0.8.7
pyenchant >=3.1.1
sphinx >=5
sphinx-autodoc-annotation *
sphinx-autodoc-typehints >=1.10.3
sphinx-gallery *
sphinx_copybutton *
sphinx_design >=0.3.0
sphinxcontrib-bibtex >=2.3.0
sphinxcontrib-spelling *

requirements.txt pypi

anndata >=0.8,<0.9
docrep >=0.3.0
joblib >=0.13.1
matplotlib >=3.3.0
networkx >=2.2
numba >=0.51.0
numpy >=1.17.0
pandas >=1.3.0,
pygam >=0.8.0
pygpcca >=1.0.3
scanpy >=1.7.2
scikit-learn >=0.24.0
scipy >=1.2.0
scvelo >=0.2.4
seaborn >=0.10.0
setuptools >=41.0.1
wrapt >=1.12.1

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/theislab/cellrank

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: cellrank

Rankings

Maintainers (3)

Dependencies