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 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
7 of 26 committers (26.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.5%) to scientific vocabulary
Keywords
data-structures
genomicranges
genomics
pandas
python
Keywords from Contributors
bioinformatics
distribution
interactive
sequences
generic
projection
standardization
optim
embedded
observability
Last synced: 6 months ago
·
JSON representation
Repository
Performant Pythonic GenomicRanges
Basic Info
- Host: GitHub
- Owner: pyranges
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://pyranges.readthedocs.io
- Size: 7.66 MB
Statistics
- Stars: 485
- Watchers: 12
- Forks: 50
- Open Issues: 91
- Releases: 7
Topics
data-structures
genomicranges
genomics
pandas
python
Created almost 8 years ago
· Last pushed 11 months ago
Metadata Files
Readme
Changelog
License
Code of conduct
README.md
pyranges
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data, particularly genomic intervals (like genes, genomic features, or reads). The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, is available at https://pyranges.readthedocs.io/
Features
- fast
- memory-efficient
- featureful
- pythonic/pandastic
- supports chaining with a terse syntax
- uses Pandas DataFrames, so the whole Python data science stack works on PyRanges
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919 http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
- most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
- use pyranges in Stack Overflow/biostars questions and answers
- star the repo (possibly important for github visibility and as a proxy for project popularity)
- if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
Asking for help
If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues
Contributing to pyranges
Pyranges accepts code contributions in form of pull request. For details, visit https://pyranges.readthedocs.io/developer_guide.html
Owner
- Name: pyranges
- Login: pyranges
- Kind: organization
- Repositories: 5
- Profile: https://github.com/pyranges
GitHub Events
Total
- Issues event: 10
- Watch event: 38
- Issue comment event: 30
- Push event: 3
- Pull request event: 4
- Fork event: 4
Last Year
- Issues event: 10
- Watch event: 38
- Issue comment event: 30
- Push event: 3
- Pull request event: 4
- Fork event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Endre Bakken Stovner | e****5@g****m | 397 |
| Endre Bakken Stovner | e****k@b****l | 36 |
| Endre Bakken Stovner | e****k@E****n | 22 |
| endre bakken stovner | e****r@d****o | 16 |
| endre bakken stovner | e****r@e****l | 14 |
| Marco Mariotti | m****m@g****m | 9 |
| Johnny Li | i****i@m****u | 3 |
| endre bakken stovner | e****r@d****o | 3 |
| endre bakken stovner | e****r@d****o | 2 |
| Fairlie Reese | f****k@c****t | 2 |
| endre bakken stovner | e****r@e****n | 2 |
| Endre Bakken Stovner | e****k@d****o | 2 |
| Amin Allahyar | a****w@g****m | 1 |
| Endre Bakken Stovner | e****k@d****o | 1 |
| Muhammed Hasan | m****k@g****m | 1 |
| Li Yao | y****5@o****m | 1 |
| Masahiro Kanai | C****t@g****m | 1 |
| Chang Y | y****0@g****m | 1 |
| Fairlie Reese | f****e@g****m | 1 |
| Chris Friedline | c****s@f****t | 1 |
| Wouter De Coster | d****r@g****m | 1 |
| Muhammed Hasan | h****k@s****r | 1 |
| dependabot[bot] | 4****] | 1 |
| SamBryce-Smith | 4****h | 1 |
| Greg Slodkowicz | j****h | 1 |
| FabrizioG202 | 5****2 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 47
- Total pull requests: 39
- Average time to close issues: 9 months
- Average time to close pull requests: about 2 months
- Total issue authors: 31
- Total pull request authors: 10
- Average comments per issue: 3.47
- Average comments per pull request: 0.72
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 3
Past Year
- Issues: 5
- Pull requests: 6
- Average time to close issues: about 8 hours
- Average time to close pull requests: 13 days
- Issue authors: 5
- Pull request authors: 4
- Average comments per issue: 2.6
- Average comments per pull request: 3.17
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- marco-mariotti (7)
- endrebak (6)
- fairliereese (2)
- brian-arnold (2)
- leetaiyi (2)
- dvmcconnell (1)
- hardingnj (1)
- jnasser3 (1)
- violafanfani (1)
- BeyondTheProof (1)
- duncster94 (1)
- wdecoster (1)
- Jeltje (1)
- alexlenail (1)
- michaelJwilson (1)
Pull Request Authors
- endrebak (23)
- marco-mariotti (5)
- dependabot[bot] (4)
- Isy89 (2)
- yfarjoun (2)
- maclandrol (2)
- semenko (2)
- y9c (2)
- tomwardio (1)
- fairliereese (1)
Top Labels
Issue Labels
enhancement (10)
good first issue (3)
help wanted (1)
cookbook (1)
Pull Request Labels
dependencies (4)
Packages
- Total packages: 1
-
Total downloads:
- pypi 25,375 last-month
- Total docker downloads: 3,881
- Total dependent packages: 56
- Total dependent repositories: 56
- Total versions: 123
- Total maintainers: 2
pypi.org: pyranges
GenomicRanges for Python.
- Homepage: http://github.com/pyranges/pyranges
- Documentation: https://pyranges.readthedocs.io/
- License: MIT
-
Latest release: 0.1.4
published 11 months ago
Rankings
Dependent packages count: 0.3%
Docker downloads count: 1.2%
Dependent repos count: 2.0%
Average: 2.7%
Downloads: 3.3%
Stargazers count: 3.4%
Forks count: 6.3%
Last synced:
6 months ago
Dependencies
docs/requirements.txt
pypi
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- sphinxcontrib-napoleon *
setup.py
pypi
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.github/workflows/build-book.yml
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actions
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- pypa/gh-action-pypi-publish v1.5.0 composite
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actions
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actions
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pyproject.toml
pypi
- natsort *
- ncls >=0.0.63
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- sorted_nearest >=0.0.33
- tabulate *