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thoraxe

Use Thor's Axe to cut exons into their evolutionary building blocks :zap:

https://github.com/phylosofs-team/thoraxe

Science Score: 57.0%

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
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords

alternative-splicing bioinformatics exon homology orthology-inference protein-evolution
Last synced: 6 months ago · JSON representation ·

Repository

Use Thor's Axe to cut exons into their evolutionary building blocks :zap:

Basic Info
Statistics
  • Stars: 12
  • Watchers: 2
  • Forks: 5
  • Open Issues: 5
  • Releases: 9
Topics
alternative-splicing bioinformatics exon homology orthology-inference protein-evolution
Created about 7 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

ThorAxe

Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs

Status |Linux |Windows
:-------------------------:|:-------------------------|:------------------------- Project Status: Inactive The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows. | Build Status
Coverage Status | Build status
codecov

Please refer to the documentation for installation instructions and more information.

Check out our video tutorial to see how you can easily use ThorAxe and visualise the results! If you want to know more, you can read our Genome Research publication:

Zea DJ, Laskina S, Baudin A, Richard H, Laine E. Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Research. 2021 Jun 15:gr-274696. doi: 10.1101/gr.274696.120.

You can install ThorAxe from PyPI and run it locally. You can also use our Docker image or run it online with interactive outputs thanks to the Ases web server.

Owner

  • Name: MASSIV
  • Login: PhyloSofS-Team
  • Kind: organization

Citation (CITATION.bib) 

@article{zea2021assessing,
  title={Assessing conservation of alternative splicing with evolutionary splicing graphs},
  author={Zea, Diego Javier and Laskina, Sofya and Baudin, Alexis and Richard, Hugues and Laine, Elodie},
  journal={Genome Research},
  volume={31},
  number={8},
  pages={1462--1473},
  year={2021},
  publisher={Cold Spring Harbor Lab}
}

GitHub Events

Total
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 5
  • Push event: 2
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 2
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 5
  • Push event: 2
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 2
  • Create event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 477
  • Total Committers: 4
  • Avg Commits per committer: 119.25
  • Development Distribution Score (DDS): 0.023
Top Committers
Name Email Commits
Diego Javier Zea d****a@g****m 466
Elodie Laine e****e@u****r 5
Diego Javier Zea e****a@g****m 4
Hugues Richard h****d@u****r 2
Committer Domains (Top 20 + Academic)
upmc.fr: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 6
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 25 days
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: about 10 hours
  • Average time to close pull requests: 1 minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zpliu1126 (1)
  • josephhughes (1)
  • kuangzhuoran (1)
  • 377079200 (1)
  • huguesrichard (1)
Pull Request Authors
  • elolaine (4)
  • dependabot[bot] (3)
  • zpliu1126 (2)
  • LouisCarrelB (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 18 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 16
  • Total maintainers: 1
pypi.org: thoraxe

Disentangle homology relationships between exons.

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 18 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 19.1%
Stargazers count: 20.3%
Dependent repos count: 21.7%
Average: 22.2%
Downloads: 39.9%
Maintainers (1)
diegozea
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • biopython ==1.77
  • certifi ==2020.6.20
  • chardet ==3.0.4
  • decorator ==4.4.2
  • idna ==2.10
  • networkx ==2.4
  • numpy ==1.19.0
  • pandas ==1.0.5
  • python-dateutil ==2.8.1
  • pytz ==2020.1
  • recordclass ==0.13.2
  • requests ==2.24.0
  • six ==1.15.0
  • urllib3 ==1.25.9
setup.py pypi
  • biopython >1.44,<1.78
  • networkx ==2.3.0
  • numpy <1.20
  • pandas >0.21.0
  • recordclass *
  • requests *
  • tabulate *
  • urllib3 >=1.26.5
Dockerfile docker
  • ubuntu bionic build
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • peaceiris/actions-gh-pages v3 composite