R Observatory: Metrics for bedr version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bedr

1.1.5

Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

2packages depend

12.5Kdownloads / year

21.3%test coverage

13/13checks pass

Overview

About

Maintained by Paul C. BoutrosFirst published 2015-09-049 releasesCRAN page ↗GitHub ↗

Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bedr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("theboutroslab/package-bedr")

Development version from theboutroslab/package-bedr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bedr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bedr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bedr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.34

21.3%

Coverage · measured lines

0%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 76%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 60%

Downloads

12.5K

CRAN downloads in the past year

Rank #4,823 · ~34/day · ~1K/mo

Releases R versions

Daily download trend is not available in this view yet.

37530 days

1.6K90 days

12.5K1 year

Compare downloads with other packages →

Also on290 r2u52 autocran2.7K conda_forge311 bioconda

Repository

GitHub ↗ theboutroslab/package-bedr

0Stars

0Forks

0Open issues

0Open PRs

0Releases

License GPL-2.0 · Last activity 2026-03-18

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/theboutroslab/package-bedr on 2026-08-16.

Continuous integration (1)

GitHub Actions

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0

Imports (7)

testthat VennDiagram data.table (>= 1.8.11)R.utils yamlparallelgrid

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Ravages chicane

Code & Tests

People & History

People (9)

Maintainer (1)

Paul C. Boutros

Author, Maintainer, Copyright holder

Authors (3)

Paul C. Boutros

Author, Maintainer, Copyright holder

Syed Haider

Author

Daryl Waggott

Author

Contributors (6)

Michael Chirico

Contributor · added in 1.1.3

Clement Fung

Contributor

Dan Knight

Contributor · added in 1.1.3

Emilie Lalonde

Contributor

Melinda Luo

Contributor · added in 1.1.3

Helena Winata

Contributor · added in 1.1.3

Copyright holders (1)

Paul C. Boutros

Author, Maintainer, Copyright holder

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
2026-01-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.3
2025-04-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.7
2019-04-01 · diff ↗
1.0.6
2019-01-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.4
2017-10-13 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.3
2016-08-23 · diff ↗

Show 5 earlier events

R
R 3.3.0 released · 2016-05-03
1.0.2
2015-09-21 · diff ↗
1.0.1
2015-09-05 · diff ↗
1.0.0
2015-09-04
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-09-04
Total releases: 9 / 11 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.0
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bedr")

Format

C. Boutros, P., Chirico, M., Fung, C., Haider, S., Knight, D., Lalonde, E., Luo, M., Waggott, D., & Winata, H. (2026). bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix' (Version 1.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.bedr

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for bedr version 1.1.5 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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