run-dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Science Score: 36.0%
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
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✓DOI references
Found 9 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
10 of 19 committers (52.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Keywords
Repository
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Basic Info
- Host: GitHub
- Owner: linnabrown
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: http://bcb.unl.edu/dbCAN2
- Size: 155 MB
Statistics
- Stars: 152
- Watchers: 6
- Forks: 40
- Open Issues: 0
- Releases: 9
Topics
Metadata Files
README.md
run_dbcan - Standalone Tool of dbCAN3
News and Updates
- [2025.4.22] 🔥 This
run_dbcanproject is not maintained under this repo and has been moved to bcb-unl/run_dbcan. This repo will be archived and go to read-only mode.
Introduction
run_dbcan is the standalone version of the dbCAN3 annotation tool for automated CAZyme annotation. This tool, known as run_dbcan, incorporates HMMER, Diamond, and dbCAN_sub for annotating CAZyme families, and integrates Cazyme Gene Clusters (CGCs) and substrate predictions.
For usage discussions, visit our issue tracker. To learn more, read the dbcan doc. If you're interested in contributing, whether through issues or pull requests, please review our contribution guide.
Reference
Please cite the following dbCAN publications if you use run_dbcan in your research:
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin,
Nucleic Acids Research, 2023;, gkad328, doi: 10.1093/nar/gkad328.
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin
Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101, doi: 10.1093/nar/gky418.
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation
Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin
Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D516–D521, doi: 10.1093/nar/gkx894*.
Owner
- Name: Le Huang
- Login: linnabrown
- Kind: user
- Location: Chapel Hill, NC
- Company: University of North Carolina
- Website: https://linnabrown.github.io
- Twitter: LeHuang9
- Repositories: 2
- Profile: https://github.com/linnabrown
Computational Biology PhD Student @ UNC
GitHub Events
Total
- Issues event: 49
- Watch event: 11
- Member event: 1
- Issue comment event: 30
- Push event: 2
- Pull request event: 3
- Fork event: 4
Last Year
- Issues event: 49
- Watch event: 11
- Member event: 1
- Issue comment event: 30
- Push event: 2
- Pull request event: 3
- Fork event: 4
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| linnabrown | l****g@u****u | 135 |
| huangle | 5****0@q****m | 89 |
| HaidYi | h****i@c****u | 31 |
| Qiwei Ge | 3****e | 17 |
| Le Huang | l****g@m****u | 15 |
| linnabrown | 2****9@m****n | 8 |
| linnabrown | l****g@l****u | 7 |
| linnabrown | l****g@u****c | 7 |
| Yanbin Yin | y****n@u****u | 6 |
| linnabrown | 2****9@m****m | 4 |
| yinlabniu | y****n@n****u | 4 |
| HD Yi | 9****4@q****m | 2 |
| Simon Guest | s****t@t****g | 2 |
| pooranis | p****s | 2 |
| Aaron Oliver | a****r@u****u | 1 |
| haidyi | h****i@h****l | 1 |
| Dongyao Li | 5****e | 1 |
| Alex Fraser | 7****r | 1 |
| linnabrown | l****g@c****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 146
- Total pull requests: 35
- Average time to close issues: 8 months
- Average time to close pull requests: 21 days
- Total issue authors: 112
- Total pull request authors: 11
- Average comments per issue: 4.21
- Average comments per pull request: 0.66
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 9
- Pull requests: 4
- Average time to close issues: 16 days
- Average time to close pull requests: about 2 months
- Issue authors: 9
- Pull request authors: 2
- Average comments per issue: 1.56
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Rob-murphys (9)
- Jigyasa3 (4)
- SilasK (3)
- trx296554555 (3)
- Russel88 (2)
- cmkobel (2)
- LuDeChen (2)
- lherold1 (2)
- adityabandla (2)
- szzxpxf (2)
- Panda-smile (2)
- BinhongLiu (2)
- Anqi-Dai (2)
- tgurbich (2)
- justinshaffer (2)
Pull Request Authors
- linnabrown (18)
- HaidYi (13)
- Xinpeng021001 (8)
- QiweiGe (3)
- Li-Dongyao-ancore (2)
- AlexSCFraser (1)
- tesujimath (1)
- AaronAOliver (1)
- ghost (1)
- chtsai0105 (1)
- pooranis (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 50 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 14
- Total maintainers: 2
pypi.org: run-dbcan
Standalone version of dbCAN annotation tool for automated CAZyme annotation
- Homepage: https://github.com/linnabrown/run_dbcan
- Documentation: https://run-dbcan.readthedocs.io/
- License: GPLv3
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Latest release: 3.0.0
published about 4 years ago
Rankings
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- conda/miniconda3 latest build
- natsort *
- numpy *
- psutil *
- scipy *
- setuptools *