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Open Source Science

https://github.com/databio/pepatac

A modular, containerized pipeline for ATAC-seq data processing

https://github.com/databio/pepatac

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 15 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary

Keywords from Contributors

bioinformatics bioinformatics-pipeline ngs pipeline-submission-engine reproducibility
Last synced: 7 months ago · JSON representation

Repository

A modular, containerized pipeline for ATAC-seq data processing

Basic Info
  • Host: GitHub
  • Owner: databio
  • License: bsd-2-clause
  • Language: Python
  • Default Branch: master
  • Homepage: http://pepatac.databio.org
  • Size: 21.8 MB
Statistics
  • Stars: 57
  • Watchers: 21
  • Forks: 16
  • Open Issues: 57
  • Releases: 47
Created almost 10 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

pepatac logo



PEP compatible

PEPATAC is a pipeline for ATAC-seq data. For more information see: http://pepatac.databio.org/

Docs

Develop docs with:

mkdocs serve -f mkdocs.yml

Build and deploy with:

mkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/pepatac/

Contributing

Pull requests welcome. Active development should occur in a development or feature branch.

Contributors

  • Jason Smith, jasonsmith@virginia.edu
  • Nathan Sheffield, nathan@code.databio.org
  • Jin Xu, jinxu9@stanford.edu
  • Ryan Corces, rcorces@stanford.edu
  • Vince Reuter, vreuter@protonmail.com
  • Donald Campbell, https://github.com/donaldcampbelljr
  • Others... (add your name)

Citing

If you find PEPATAC useful in your research, please cite:

Jason P. Smith, M. Ryan Corces, Jin Xu, Vincent P. Reuter, Howard Y. Chang, and Nathan C. Sheffield. PEPATAC: An optimized ATAC-seq pipeline with serial alignments. bioRxiv (2021). DOI: 10.1101/2020.10.21.347054

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
  • Create event: 6
  • Release event: 5
  • Issues event: 16
  • Watch event: 4
  • Delete event: 1
  • Issue comment event: 53
  • Push event: 49
  • Pull request review event: 1
  • Pull request event: 18
  • Fork event: 2
Last Year
  • Create event: 6
  • Release event: 5
  • Issues event: 16
  • Watch event: 4
  • Delete event: 1
  • Issue comment event: 53
  • Push event: 49
  • Pull request review event: 1
  • Pull request event: 18
  • Fork event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 1,400
  • Total Committers: 15
  • Avg Commits per committer: 93.333
  • Development Distribution Score (DDS): 0.434
Past Year
  • Commits: 67
  • Committers: 4
  • Avg Commits per committer: 16.75
  • Development Distribution Score (DDS): 0.075
Top Committers
Name Email Commits
jpsmith5 j****h@v****u 792
nsheff n****f 347
Vince Reuter v****r@g****m 98
Donald Campbell 1****r 93
jinxu937 j****9@s****u 25
Michal Stolarczyk s****3@g****m 21
Ryan Corces r****s@g****m 14
carbonwei y****6@s****u 3
Florian Halbritter f****r 1
John Lawson j****n 1
ayobi 1****i 1
jf2016GH j****a@y****m 1
sunta3iouxos s****s@g****m 1
syntonym s****r@g****m 1
andy 1****2 1
Committer Domains (Top 20 + Academic)
stanford.edu: 2 virginia.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 174
  • Total pull requests: 51
  • Average time to close issues: 5 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 66
  • Total pull request authors: 9
  • Average comments per issue: 3.67
  • Average comments per pull request: 0.59
  • Merged pull requests: 45
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 19
  • Pull requests: 19
  • Average time to close issues: 18 days
  • Average time to close pull requests: 9 days
  • Issue authors: 13
  • Pull request authors: 3
  • Average comments per issue: 3.26
  • Average comments per pull request: 0.26
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nsheff (49)
  • rcorces (21)
  • donaldcampbelljr (7)
  • gbloeb (5)
  • zhongzheng1999 (4)
  • lmckinno (3)
  • DavideBrex (3)
  • wangjiawen2013 (3)
  • hiroyukikato911 (3)
  • sunta3iouxos (3)
  • carbonwei (3)
  • yqlan (2)
  • shmilyfhh (2)
  • victorwang123 (2)
  • moor2562 (2)
Pull Request Authors
  • donaldcampbelljr (28)
  • nsheff (12)
  • jpsmith5 (6)
  • syntonym (4)
  • vreuter (4)
  • fbnrst (2)
  • sunta3iouxos (2)
  • ccrobertson (1)
  • rcorces (1)
Top Labels
Issue Labels
bug (12) enhancement (10) question (8) docs (6) likely-solved (6) priority - high (3) priority-low (1)
Pull Request Labels

Dependencies

PEPATACr/DESCRIPTION cran
  • GenomicDistributions * depends
  • R >= 3.5.1 depends
  • data.table * depends
  • ggplot2 * depends
  • gplots * depends
  • grid * depends
  • optigrab * depends
  • pepr * depends
  • scales * depends
requirements-docs.txt pypi
  • fontawesome-markdown *
requirements-test.txt pypi
  • pytest ==3.1.3 test
requirements.txt pypi
  • Cython >=0.29
  • MACS2 >=2.2.7.1
  • attmap >=0.13.0
  • bio >=0.2.4
  • codecov >=2.0
  • colorama >=0.3.9
  • cykhash >=1.0.2
  • divvy >=0.6.0
  • eido >=0.1.5
  • hypothesis ==4.38.0
  • jinja2 *
  • jsonschema >=3.0.1
  • logmuse >=0.2.6
  • looper >=1.3.1
  • numpy >=1.21
  • oyaml *
  • pandas >=1.4
  • pararead >=0.7.0
  • peppy >=0.31.1
  • piper >=0.12.3
  • psutil >=5.8
  • pysam >=0.16
  • python-Levenshtein >=0.12
  • pyyaml >=3.13
  • refgenconf >=0.12.2
  • ubiquerg >=0.6.1
  • yacman >=0.8.4