bedr

1.1.5

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

2packages depend

12.8Kdownloads / 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)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

# 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: 5.7 min · r-oldrel-windows-x86_64

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

12.8K

CRAN downloads in the past year

Rank #5,369 · ~35/day · ~1.1K/mo

bedr Releases R versions

Daily download trend is not available in this view yet.

54430 days

1.7K90 days

12.8K1 year

Compare downloads with other packages →

Also on284 r2u62 autocran2.6K conda_forge319 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 2026-07-19.

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

Paul C. Boutros

Author, Maintainer, Copyright holder

Package Timeline

9 releases. 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
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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