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nucleoatac

nucleosome calling using ATAC-seq

https://github.com/greenleaflab/nucleoatac

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary

Keywords

atac-seq bioinformatics nuclesosome
Last synced: 6 months ago · JSON representation

Repository

nucleosome calling using ATAC-seq

Basic Info
  • Host: GitHub
  • Owner: GreenleafLab
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 15 MB
Statistics
  • Stars: 106
  • Watchers: 18
  • Forks: 31
  • Open Issues: 26
  • Releases: 0
Topics
atac-seq bioinformatics nuclesosome
Created almost 11 years ago · Last pushed about 5 years ago
Metadata Files
Readme License

README.md

NucleoATAC

This package is no longer being actively maintained; feel free to post issues that others in the community may respond to, but this package will likely not be updated further. Additionally, if anyone wants to maintain a fork of the package or has developed an alternative package for similar purposes, would be happy to link to that repo here.

Python package for calling nucleosomes using ATAC-seq data. Also includes general scripts for working with paired-end ATAC-seq data (or potentially other paired-end data).

Please cite our paper at Genome Research if you use this tool in your research.

Please use GitHub Issues to bring up any errors that occur with software rather than emailing authors.

Note on Versions:

  • version 0 represents code used for biorxiv manuscript
  • version 0.2.1 was used for Genome Research manuscript (See Supplemental Information as well)

Documentation can be found at http://nucleoatac.readthedocs.org/en/latest/

If you want to easily read in NucleoATAC outputs into R for further processing or exploration, check out NucleoATACR

Currently NucleoATAC only supports Python 2.7 (No Python 3). If anyone is interested in adding Python 3 support, pull requests welcome :smile:

Owner

  • Name: GreenleafLab
  • Login: GreenleafLab
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 113
  • Total Committers: 2
  • Avg Commits per committer: 56.5
  • Development Distribution Score (DDS): 0.044
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alicia Schep a****p@s****u 108
Alicia Schep a****p@g****m 5
Committer Domains (Top 20 + Academic)
stanford.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 92
  • Total pull requests: 6
  • Average time to close issues: 4 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 69
  • Total pull request authors: 2
  • Average comments per issue: 2.66
  • Average comments per pull request: 0.83
  • Merged pull requests: 5
  • 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
  • PFRoux (4)
  • OscarBrock (4)
  • ShaluJhanwar (4)
  • igordot (3)
  • juechenyang (2)
  • crazyhottommy (2)
  • ghost (2)
  • hmyh1202 (2)
  • duyphamuab (2)
  • will-NYGC (2)
  • antgomo (2)
  • evanbiederstedt (2)
  • mbaddoo (2)
  • Angrydutchman (2)
  • krouskas (2)
Pull Request Authors
  • AliciaSchep (5)
  • oaxiom (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 23 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 15
  • Total maintainers: 1
proxy.golang.org: github.com/greenleaflab/nucleoatac
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/GreenleafLab/NucleoATAC
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 6 months ago
pypi.org: nucleoatac

python package for calling nucleosomes with ATAC-Seq

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 23 Last month
Rankings
Stargazers count: 7.2%
Forks count: 7.3%
Dependent packages count: 10.0%
Average: 19.2%
Dependent repos count: 21.7%
Downloads: 49.9%
Maintainers (1)
aschep
Last synced: 6 months ago