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ciriquant

circular RNA quantification tools

https://github.com/bioinfo-biols/ciriquant

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.0%) to scientific vocabulary

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability genomics embedded
Last synced: 11 months ago · JSON representation

Repository

circular RNA quantification tools

Basic Info
Statistics
  • Stars: 31
  • Watchers: 2
  • Forks: 18
  • Open Issues: 35
  • Releases: 9
Created over 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

CIRIquant

Build Status GitHub release (latest by date) The MIT License GitHub All Releases SourceForge Documentation Status

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

Documentation

Documentation is available online at https://ciri-cookbook.readthedocs.io/en/latest/

Author

Authors: Jinyang Zhang(zhangjinyang@biols.ac.cn), Fangqing Zhao(zhfq@biols.ac.cn)

Maintainer: Jinyang Zhang

Release Notes

  • Version 1.1: Added support for stranded library and GFF3 format input.
  • Version 1.0: The first released version of CIRIquant.

License

The code is released under the MIT License. See the LICENSE file for more detail.

Citing CIRIquant

  • Zhang, J., Chen, S., Yang, J. et al. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11, 90 (2020) doi:10.1038/s41467-019-13840-9

Owner

  • Name: Fangqing Zhao's Lab
  • Login: bioinfo-biols
  • Kind: organization
  • Email: zhfq@biols.ac.cn
  • Location: Beijing

Genomics & Computational Biology Lab, Beijing Institutes of Life Science

GitHub Events

Total
  • Issues event: 6
  • Watch event: 3
  • Issue comment event: 13
  • Fork event: 1
Last Year
  • Issues event: 6
  • Watch event: 3
  • Issue comment event: 13
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 92
  • Total Committers: 5
  • Avg Commits per committer: 18.4
  • Development Distribution Score (DDS): 0.076
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kevinzjy k****7@g****m 85
Barry digby b****7@g****m 2
dependabot[bot] 4****] 2
Jinyang Zhang z****y@J****l 2
osagiei o****e@e****k 1
Committer Domains (Top 20 + Academic)
ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 70
  • Total pull requests: 7
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 29 days
  • Total issue authors: 50
  • Total pull request authors: 4
  • Average comments per issue: 2.69
  • Average comments per pull request: 1.14
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 8
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 7
  • Pull request authors: 2
  • Average comments per issue: 0.88
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • DarioS (5)
  • prisca399 (4)
  • algaebrown (3)
  • andre-gabriel-42 (3)
  • solo7773 (2)
  • mysolid23 (2)
  • Kevinzjy (2)
  • junjunlab (2)
  • stefanerb89 (2)
  • choijamtsmunkhzul (2)
  • gnilihzeux (2)
  • eltonjrv (2)
  • mlvanhorn (2)
  • non-ascii (1)
  • gkibt (1)
Pull Request Authors
  • dependabot[bot] (5)
  • nictru (2)
  • osagiei (1)
  • BarryDigby (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels
dependencies (5)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 87 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 7
  • Total maintainers: 1
pypi.org: ciriquant

circular RNA quantification pipeline

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 87 Last month
Rankings
Forks count: 9.6%
Dependent packages count: 10.0%
Dependent repos count: 11.6%
Average: 11.6%
Stargazers count: 12.4%
Downloads: 14.4%
Maintainers (1)
kevinzjy
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • PyYAML ==5.4
  • argparse >=1.2.1
  • numexpr ==2.6.9
  • numpy ==1.22.0
  • pysam ==0.15.2
  • scikit-learn ==0.20.3
  • scipy ==1.2.2
setup.py pypi
  • PyYAML ==5.4
  • argparse >=1.2.1
  • numexpr ==2.6.9
  • numpy ==1.22.0
  • pysam ==0.15.2
  • scikit-learn ==0.20.3
  • scipy ==1.2.2