BED

1.6.3

Biological Entity Dictionary (BED)

1packages depend

4.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Patrice GodardFirst published 2021-01-0512 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 98%
Return-value docs: 81%
References docs: 0%

Downloads

4.2K

CRAN downloads in the past year

Rank #9,872 · ~12/day · ~353/mo

Releases R versions

Daily download trend is not available in this view yet.

38630 days

1.1K90 days

4.2K1 year

Compare downloads with other packages →

Also on589 r2u72 autocran20 c2d4u

Repository

GitHub ↗ patzaw/bed

8Stars

4Forks

2Open issues

0Open PRs

19Releases

267Commits

2Contributors

License GPL-3.0 · 267 commits · Last activity 2026-06-29

Stars over time

2023-01-29 · 72026-07-07 · 8

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/patzaw/bed on 2026-07-19.

Docs source (1)

README.Rmd

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

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

1direct

0indirect

TKCat

Code & Tests

Code Composition

R 12,881 (74%)Rd 3,474 (20%)Vignettes 868 (5%)C 183 (1%)

Code characteristics

Object systems

S314

Cyclomatic complexity: 3.0 median / 42 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

124 59 exported

Complexity

7.4 avg / 42 max

Call network

124 nodes / 264 edges

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Patrice Godard

Author, Maintainer, Copyright holder

Authors (1)

Patrice Godard

Author, Maintainer, Copyright holder

Patrice Godard

Author, Maintainer, Copyright holder

Package Timeline

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

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

1.4.4
2021-03-12 · diff ↗
1.4.3
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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