R Observatory: Metrics for BED version 1.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BED

1.6.3

Biological Entity Dictionary (BED)

0packages dependsuggested by 1

4.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Patrice GodardCRAN page ↗GitHub ↗Website ↗Issues ↗

An interface for the 'Neo4j' database providing mapping between different identifiers of biological entities. This Biological Entity Dictionary (BED) has been developed to address three main challenges. The first one is related to the completeness of identifier mappings. Indeed, direct mapping information provided by the different systems are not always complete and can be enriched by mappings provided by other resources. More interestingly, direct mappings not identified by any of these resources can be indirectly inferred by using mappings to a third reference. For example, many human Ensembl gene ID are not directly mapped to any Entrez gene ID but such mappings can be inferred using respective mappings to HGNC ID. The second challenge is related to the mapping of deprecated identifiers. Indeed, entity identifiers can change from one resource release to another. The identifier history is provided by some resources, such as Ensembl or the NCBI, but it is generally not used by mapping tools. The third challenge is related to the automation of the mapping process according to the relationships between the biological entities of interest. Indeed, mapping between gene and protein ID scopes should not be done the same way than between two scopes regarding gene ID. Also, converting identifiers from different organisms should be possible using gene orthologs information. The method has been published by Godard and van Eyll (2018) doi:10.12688/f1000research.13925.3.

Install

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

install.packages("BED", 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("patzaw/BED")

Development version from patzaw/BED. 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-bed

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-BED

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-BED

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: 3.1 min · r-devel-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 1.6.3

README· In the repository, left out of the releaseVignettesYes · 1 · evaluation depends on the environmentNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 98
Examples that run: 0%29 never run
Exported functions with examples: 51%
Documented parameters: 98%
Return-value docs: 81%
Help pages citing references: 0%

Vignettes (1)

BED

How these are measured

Downloads

4.5K

CRAN downloads in the past year

Rank #5,875 · ~12/day · ~373/mo

Releases R versions

Daily download trend is not available in this view yet.

54230 days

1.4K90 days

4.5K1 year

Compare downloads with other packages →

Also on549 r2u44 autocran57 c2d4u

How downloads are counted

Repository

patzaw/bed ↗Account: patzaw

8Stars

4Forks

2Open issues

0Open PRs

19Releases

268Commits

2Commit identities

License file reads as GPL-3.0 · 268 commits · Last activity 2026-10-10

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: 0

Stars over time

2023-01-29 · 72026-07-07 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/patzaw/bed on 2026-10-11.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-10

pkgdown site last built 2026-10-10

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing BED adds 71 packages (37 with compiled code, 54 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, visNetwork 4.1 MB.

Depends (3)

R >= 3.6neo2R visNetwork

Imports (9)

dplyr readr stringrutilsshiny htmltools DT miniUI rstudioapi

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown biomaRt GEOquery base64enc webshot2 RCurl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

TKCat

How these are counted

Code & Tests

People & History

People (1)

Patrice Godard

Releases (12)

Pick two releases to compare their code metrics.

1.6.3Latest
record
2026-06-29 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.6.2
record
2025-06-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.0
record
2024-11-09 · diff ↗
1.5.2
record
2024-05-22 · diff ↗
1.5.1
record
2024-04-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.5.0
record
2024-01-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.13
record
2023-03-02 · diff ↗
1.4.12
record
2023-02-16 · diff ↗
1.4.11
record
2022-11-07 · diff ↗
1.4.8
record
2022-04-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18

Show 3 earlier eventsHide 3 earlier events

1.4.4
record
2021-03-12 · diff ↗
1.4.3
record
2021-01-05
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-05
Total releases: 12 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Download size: 1.5 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("BED")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.12688/f1000research.13925.3.

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 BED version 1.6.3 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →