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bedops

:microscope: BEDOPS: high-performance genomic feature operations

https://github.com/bedops/bedops

Science Score: 54.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 18 committers (27.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary

Keywords

bed bedops bioinformatics c c-plus-plus compression conversion genomics parallel pipeline set set-theory toolkit
Last synced: 4 months ago · JSON representation ·

Repository

:microscope: BEDOPS: high-performance genomic feature operations

Basic Info
Statistics
  • Stars: 351
  • Watchers: 16
  • Forks: 62
  • Open Issues: 20
  • Releases: 0
Topics
bed bedops bioinformatics c c-plus-plus compression conversion genomics parallel pipeline set set-theory toolkit
Created over 12 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Citation

README.md

BEDOPS v2.4.42: high-performance genomic feature operations

GitHub stars Project license <!-- -->

About

BEDOPS v2.4.42 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.42 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

Downloads

Linux Source code

Documentation

Complete documentation for BEDOPS v2.4.42 tools is available at: https://bedops.readthedocs.io/

Citation

If you use BEDOPS v2.4.42 in your research, please cite the following manuscript:

Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
BEDOPS: high-performance genomic feature operations
Bioinformatics (2012) 28 (14): 1919-1920.

Copyright

Copyright (C) 2011-2025 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds

Source code, documentation and media assets released under GNU Public License Version 2 (GPL v2).

Owner

  • Name: BEDOPS
  • Login: bedops
  • Kind: user
  • Location: Seattle, WA
  • Company: Altius Institute for Biomedical Sciences

Citation (CITATION.cff) 

cff-version: 1.0.3
message: If you use BEDOPS in your research, please cite the following manuscript.
title: BEDOPS
version: 2.4.42
date-released: 2022-07-21
doi: 10.1093/bioinformatics/bts277
commit: 355911acd3e474b755def3283a76151e2299049b
url: http://bedops.readthedocs.io/
repository-code: https://github.com/bedops/bedops/
license: GPL-2.0
abstract: >-
    BEDOPS is a suite of tools to address common questions raised in 
    genomic studies — mostly with regard to overlap and proximity 
    relationships between data sets. It aims to be scalable and flexible, 
    facilitating the efficient and accurate analysis and management of 
    large-scale genomic data.


authors:
  - family-names: Neph
    given-names: Shane
  - family-names: Kuehn
    given-names: M. Scott
  - family-names: Reynolds
    given-names: Alex
    orcid: https://orcid.org/0000-0003-1409-8945

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 7
  • Watch event: 44
  • Issue comment event: 5
  • Push event: 5
  • Fork event: 4
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 7
  • Watch event: 44
  • Issue comment event: 5
  • Push event: 5
  • Fork event: 4

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 1,864
  • Total Committers: 18
  • Avg Commits per committer: 103.556
  • Development Distribution Score (DDS): 0.344
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alex Reynolds a****s@g****m 1,223
sjneph s****h@g****m 275
Alex Reynolds a****s@P****l 270
Alex Reynolds a****s@d****u 29
Alex Reynolds a****s@d****u 26
Alex Reynolds a****s@p****m 9
Jemma Nelson n****s@u****u 6
Alex Reynolds a****s@d****u 4
Alex Reynolds a****s@c****l 4
Alex Reynolds a****s@s****g 4
sjn s****n@l****n 3
Alex Reynolds a****s@d****u 2
Shane Neph s****n@b****m 2
Shane Neph s****n@s****l 2
U-AlexReynolds-PC\Alex Reynolds A****s@A****) 2
Alex Reynolds a****s@f****m 1
Shane Neph p****u 1
Bitdeli Chef c****f@b****m 1
Committer Domains (Top 20 + Academic)
bitdeli.com: 1 fiddlehead.regulomecorp.com: 1 alexreynolds-pc.(none): 1 balsamea.regulomecorp.com: 1 d-69-91-186-125.dhcp4.washington.edu: 1 localhost.localdomain: 1 stamlab.org: 1 d-69-91-147-10.dhcp4.washington.edu: 1 uw.edu: 1 papillion.regulomecorp.com: 1 d-69-91-154-204.dhcp4.washington.edu: 1 d-69-91-184-235.dhcp4.washington.edu: 1

Packages

  • Total packages: 1
  • Total downloads:
    • homebrew 22 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
formulae.brew.sh: bedops

Set and statistical operations on genomic data of arbitrary scale

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 22 Last month
Rankings
Dependent packages count: 19.0%
Forks count: 22.9%
Stargazers count: 27.5%
Average: 32.9%
Downloads: 44.1%
Dependent repos count: 50.7%
Last synced: 4 months ago

Dependencies

.github/workflows/main.yml actions
  • actions/checkout v2 composite
packaging/deb/Dockerfile docker
  • debian jessie build
packaging/docker/Dockerfile docker
  • debian jessie build
packaging/rpm/Dockerfile docker
  • centos 7 build
docs/requirements.txt pypi
  • sphinx-better-theme ==0.1.4