Science Score: 49.0%
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
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
18 of 161 committers (11.2%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Single-cell analysis in Python. Scales to >100M cells.
Basic Info
- Host: GitHub
- Owner: scverse
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://scanpy.readthedocs.io
- Size: 41.1 MB
Statistics
- Stars: 2,174
- Watchers: 48
- Forks: 659
- Open Issues: 563
- Releases: 0
Topics
Metadata Files
README.md
Scanpy – Single-Cell Analysis in Python
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
Discuss usage on the scverse Discourse. Read the documentation. If you'd like to contribute by opening an issue or creating a pull request, please take a look at our contribution guide.
scanpy 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.
Citation
If you use scanpy in your work, please cite the scanpy publication as follows:
SCANPY: large-scale single-cell gene expression data analysis
F. Alexander Wolf, Philipp Angerer, Fabian J. Theis
Genome Biology 2018 Feb 06. doi: 10.1186/s13059-017-1382-0.
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
Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.
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 | |
|---|---|---|
| falexwolf | f****f@g****e | 1,115 |
| Philipp A | f****p@w****e | 605 |
| Isaac Virshup | i****p@g****m | 452 |
| Fidel Ramírez | f****z@g****m | 223 |
| Koncopd | k****d@g****m | 167 |
| Gökçen Eraslan | g****n@g****m | 88 |
| pre-commit-ci[bot] | 6****] | 82 |
| LuckyMD | m****n@i****e | 47 |
| Awni Mousa | a****a@g****m | 44 |
| giovp | g****l@g****m | 39 |
| adamgayoso | a****o | 30 |
| Ilan Gold | i****d@g****m | 25 |
| Severin Dicks | 3****7 | 24 |
| Francesco G. Brundu | f****u@g****m | 20 |
| Lukas Heumos | l****s@p****t | 19 |
| Volker Bergen | 3****n | 17 |
| Gökcen Eraslan | g****n@b****g | 15 |
| Andres Munoz | a****s@y****u | 14 |
| tobias | t****s@l****m | 13 |
| Scott Gigante | s****e@g****m | 13 |
| atarashansky | a****y@g****m | 11 |
| Jonathan Manning | j****g@e****k | 11 |
| michalk8 | 4****8 | 10 |
| Fabian Rost | f****t@p****e | 9 |
| Eljas Roellin | 6****l | 9 |
| Tom White | t****e@g****m | 7 |
| dawe | c****e@g****m | 7 |
| Marius Lange | m****e@t****e | 6 |
| LuckyMD | m****n@g****m | 5 |
| Gregor Sturm | m****l@g****e | 5 |
| and 131 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 727
- Total pull requests: 1,428
- Average time to close issues: 11 months
- Average time to close pull requests: about 1 month
- Total issue authors: 412
- Total pull request authors: 119
- Average comments per issue: 2.81
- Average comments per pull request: 1.78
- Merged pull requests: 1,100
- Bot issues: 0
- Bot pull requests: 127
Past Year
- Issues: 166
- Pull requests: 603
- Average time to close issues: 13 days
- Average time to close pull requests: 5 days
- Issue authors: 92
- Pull request authors: 37
- Average comments per issue: 0.69
- Average comments per pull request: 1.16
- Merged pull requests: 461
- Bot issues: 0
- Bot pull requests: 57
Top Authors
Issue Authors
- flying-sheep (54)
- scverse-bot (32)
- ivirshup (30)
- ilan-gold (14)
- Intron7 (10)
- wangjiawen2013 (10)
- Zethson (8)
- adamgayoso (8)
- danli349 (7)
- brianpenghe (7)
- grst (6)
- LuckyMD (6)
- giovp (6)
- alexlenail (5)
- meeseeksmachine (5)
Pull Request Authors
- flying-sheep (471)
- meeseeksmachine (352)
- pre-commit-ci[bot] (125)
- ivirshup (96)
- ilan-gold (65)
- Intron7 (43)
- Koncopd (12)
- Zethson (12)
- eroell (11)
- kaushalprasadhial (10)
- gokceneraslan (9)
- ashish615 (8)
- Sakshi-2797 (6)
- selmanozleyen (6)
- glitchheadgit (6)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 671,457 last-month
- Total docker downloads: 20,246
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Total dependent packages: 422
(may contain duplicates) -
Total dependent repositories: 526
(may contain duplicates) - Total versions: 93
- Total maintainers: 3
pypi.org: scanpy
Single-Cell Analysis in Python.
- Homepage: https://scanpy.org
- Documentation: https://scanpy.readthedocs.io/
- License: BSD License
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Latest release: 1.11.4
published 7 months ago
Rankings
Maintainers (3)
conda-forge.org: scanpy
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
- Homepage: https://scverse.org/
- License: BSD-3-Clause
-
Latest release: 1.9.1
published almost 4 years ago
Rankings
Dependencies
- anndata >=0.7.4
- h5py >=3
- joblib *
- matplotlib >=3.4
- natsort *
- networkx >=2.3
- numba >=0.41.0
- numpy >=1.17.0
- packaging *
- pandas >=1.0
- patsy *
- scikit-learn >=0.24
- scipy >=1.4
- seaborn *
- session-info *
- statsmodels >=0.10.0rc2
- tqdm *
- umap-learn >=0.3.10
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- actions/cache v4 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite