R Observatory: Metrics for bedr version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bedr

1.1.5Package record

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

2packages depend

9.7Kdownloads / year

21.3%test coverage

13/13flavors OK

Overview

About

Maintained by Paul C. BoutrosCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.1.5

Changed

Update maintainer email to pboutros@sbpdiscovery.org
Update GitHub organization from uclahs-cds to theboutroslab
Rename repository from public-R-bedr to package-bedr

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.5

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.5Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 52
Examples that run: 74%37 run in a plain check · 12 never run · 1 hold no code
Exported functions with examples: not tracked
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 60%

Vignettes (1)

bedr HTML

How these are measured

Downloads

9.7K

CRAN downloads in the past year

Rank #4,200 · ~27/day · ~807/mo

Releases R versions

Daily download trend is not available in this view yet.

63330 days

2.1K90 days

9.7K1 year

Compare downloads with other packages →

Also on328 r2u26 autocran3K conda_forge322 bioconda

How downloads are counted

Repository

theboutroslab/package-bedr ↗Organization: TheBoutrosLab

0Stars

0Forks

0Open issues

0Open PRs

0Releases

License file reads as GPL-2.0 · Last activity 2026-03-18

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/theboutroslab/package-bedr on 2026-10-21.

Continuous integration (1)

GitHub Actions

Governance and community (1)

PR template (inherited from theboutroslab)

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing bedr adds 34 packages (13 with compiled code, 13 MB of source tarballs). Heaviest: data.table 5.7 MB, fs 1.4 MB, jsonlite 1.0 MB.

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

Imports 2

Depends, Imports or LinkingTo, most downloaded first

chicane Ravages

How these are counted

Code & Tests

Datasets

People & History

People (9)

Author

Author

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

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
record
2026-01-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.3
record
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
record
2019-04-01 · diff ↗
1.0.6
record
2019-01-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.4
record
2017-10-13 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.3
record
2016-08-23 · diff ↗

Show 5 earlier eventsHide 5 earlier events

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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