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peppan

Phylogeny Enhanded Prediction of PAN-genome

https://github.com/zheminzhou/peppan

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 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.2%) to scientific vocabulary

Keywords from Contributors

bigdata mlst
Last synced: 11 months ago · JSON representation

Repository

Phylogeny Enhanded Prediction of PAN-genome

Basic Info
Statistics
  • Stars: 42
  • Watchers: 3
  • Forks: 10
  • Open Issues: 17
  • Releases: 0
Created almost 7 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.rst 

About PEPPAN
PEPPAN (Phylogeny Enhanced Pipeline for PAN-genome) is a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPAN implements a combination of tree- and synteny-based approaches to identify and exclude paralogous genes, as well as similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes.

Citation
If you use PEPPAN please cite the pre-print in BioRxiv:

Z Zhou, M Achtman (2020) "Accurate reconstruction of the pan- and core- genomes of bacteria with PEPPA" bioRxiv, doi: `https://doi.org/10.1101/2020.01.03.894154 `_

* `installation `_
* `quickstart `_
* `parameters `_
* `inputs `_
* `outputs `_

Owner

  • Name: Zhemin Zhou
  • Login: zheminzhou
  • Kind: user
  • Company: Soochow University

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 111
  • Total Committers: 4
  • Avg Commits per committer: 27.75
  • Development Distribution Score (DDS): 0.523
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zhemin Zhou z****u@w****k 53
Zhemin Zhou z****u 49
Nina Luhmann n****n@w****k 5
janepipistrelle j****e@g****m 4
Committer Domains (Top 20 + Academic)
warwick.ac.uk: 2

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 21
  • Total pull requests: 9
  • Average time to close issues: 1 day
  • Average time to close pull requests: 31 minutes
  • Total issue authors: 18
  • Total pull request authors: 2
  • Average comments per issue: 1.1
  • Average comments per pull request: 0.0
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lalalagartija (2)
  • MrTomRod (2)
  • marade (2)
  • JoyLiu19 (1)
  • verylili (1)
  • ConstantinV (1)
  • EnriqueDoster (1)
  • SWittouck (1)
  • iferres (1)
  • MartaRudzite (1)
  • matrs (1)
  • clin86 (1)
  • Tj-Idowu (1)
  • bharat1912 (1)
  • quliping (1)
Pull Request Authors
  • nluhmann (5)
  • janepipistrelle (4)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 19 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: peppan

Phylogeny Enhanded Prediction of PAN-genome https://doi.org/10.1101/2020.01.03.894154

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 19 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 10.9%
Forks count: 11.4%
Average: 16.9%
Dependent repos count: 21.7%
Downloads: 30.6%
Maintainers (1)
zheminzhou
Last synced: 11 months ago

Dependencies

setup.py pypi
  • ete3 >=3.1.1
  • numba >=0.38.0
  • numpy >=1.18.1
  • pandas >=0.24.2
  • scipy >=1.3.2