Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 15 committers (13.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.8%) to scientific vocabulary
Keywords
Repository
Java utilities for Bioinformatics
Basic Info
- Host: GitHub
- Owner: lindenb
- License: other
- Language: Java
- Default Branch: master
- Homepage: https://jvarkit.readthedocs.io/
- Size: 63.3 MB
Statistics
- Stars: 512
- Watchers: 26
- Forks: 134
- Open Issues: 54
- Releases: 9
Topics
Metadata Files
README.md
JVARKIT
Java utilities for Bioinformatics
Documentation
Documentation is available at: https://jvarkit.readthedocs.io/
Download
A pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .
Compilation
Since 2023, most tools (but not all) are now packaged into one application jvarkit.jar. Tools that were executed like java -jar toolname.jar are now executed as java -jar jvarkit.jar toolname. The documentation is not always up to date on this point.
See the documentation at https://jvarkit.readthedocs.io/.
Conda / Bioconda
A conda package created by DrYak is available at https://bioconda.github.io/recipes/jvarkit/README.html
Containers
jvarkit is available as a Singularity container under https://depot.galaxyproject.org/singularity/ . GUI/Swing applications might not work.
Author
Pierre Lindenbaum PhD
Owner
- Name: Pierre Lindenbaum
- Login: lindenb
- Kind: user
- Location: Nantes, France
- Company: INSERM
- Website: https://genomic.social/web/@yokofakun
- Twitter: yokofakun
- Repositories: 86
- Profile: https://github.com/lindenb
Institut-du-Thorax, Nantes, France.
Citation (CITATION.cff)
cff-version: "1.1.0"
abstract: "Java utilities for Bioinformatics"
authors:
- family-names: "Lindenbaum"
given-names: "Pierre"
orcid: "https://orcid.org/0000-0003-0148-9787"
doi: "10.6084/m9.figshare.1425030"
keywords:
- bioinformatics
- java
- hts
license: MIT
message: "If you use this software, please cite it using these metadata."
repository-code: "http://github.com/lindenb/jvarkit"
title: jvarkit
version: " 2024.08.25"
GitHub Events
Total
- Issues event: 9
- Watch event: 24
- Issue comment event: 37
- Push event: 102
- Fork event: 3
- Create event: 1
Last Year
- Issues event: 9
- Watch event: 24
- Issue comment event: 37
- Push event: 102
- Fork event: 3
- Create event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Pierre Lindenbaum | p****m@y****r | 2,909 |
| Pierre Lindenbaum | 3****b | 4 |
| Pierre LINDENBAUM | l****p@n****e | 4 |
| Daniel Klevebring | d****g@g****m | 2 |
| Yossi Farjoun | f****n@g****m | 2 |
| yech | y****0@g****m | 2 |
| Tom White | t****e@g****m | 1 |
| Istvan Albert | i****t@g****m | 1 |
| Pierre LINDENBAUM | l****p@I****e | 1 |
| Lennart Karssen | l****n@p****m | 1 |
| edgardomortiz | e****v@g****m | 1 |
| Tim Yates | t****s@g****m | 1 |
| Johan Dahlberg | j****g@m****e | 1 |
| Benjamin Linard | b****d@i****r | 1 |
| shisheng-1 | 2****0@q****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: about 15 hours
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 6.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: about 15 hours
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 6.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tingchenlrx (2)
- kac2053 (1)
- yfarjoun (1)
- Mahmoudy96 (1)
- CornilleAmandine (1)
- zjgbz (1)
- NailouZhang (1)
- dcopetti (1)
- indianAppl (1)
- molly-hetheringtonrauth (1)
- asaki1986 (1)
- fa8sanger (1)
- zhujiahua700403 (1)
- tiramisutes (1)
- liaochen1988 (1)
Pull Request Authors
- Shians (1)
- lanceman999 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- ubuntu 22.04 build
- mkdocs >=1.0.4
- mkdocs-material >=4.4.0
- pygments >=2.4.2
- pymdown-extensions >=6.0