R Observatory: Metrics for bedbaser version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bedbaser

Bioc current

A BEDbase client

v1.4.0 · software · Artistic License 2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.21 · Apr 16, 2025

Current · Requires R 4.6

1.0 In 3 of 49 releases 3.23

Description

A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

21 11 exported

Complexity

2.8 avg / 13 max

Call network

21 nodes / 21 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

2,030

Files

40

Compiled share

0%

Has compiled src

No

Language breakdown

R 946 (46.6%)Tests 292 (14.4%)Docs 539 (26.6%)Vignettes 253 (12.5%)

API

Exported functions

13

Internal functions

10

Recent export changes

v3.21+13 BEDbase, bb_bed_text_search, bb_beds_in_bedset +10 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.31

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

5.6%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.5.0

System requirements

–

C++ standard

–

License

Artistic License 2.0

License flags

not SPDX, not OSI

History

Versions

3

First release

2025-10-12

Latest release

2026-04-28

Avg cadence

99 days

Cold removal rate

–

Dep drift

1

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 35 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › Infrastructure › DataImport

ThirdPartyClient

People

Andres Wokaty author maintainer
NCI fnd
Levi Waldron author

At a glance

Version: 1.4.0
Category: software
License: Artistic License 2.0
Requires R: ≥ 4.6
Maintainer: Andres Wokaty
Entered: 3.21 · Apr 16, 2025
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.5.0)

Imports

AnVIL (>= 1.16.0)BiocBiocFileCacheBioccurl dplyrGenomeInfoDbBiocGenomicRangesBiochttrmethodspurrrrtracklayerBiocrlang R.utilsstatsstringr tibble tidyrtoolsutils

Suggests

BiocStyleBiocknitrliftOverBioctestthat (>= 3.0.0)withr

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bedbaser")

Format

Wokaty, A., NCI, & Waldron, L. (2026). bedbaser: A BEDbase client (Version 1.4.0) [Computer software]. https://bioconductor.org/packages/bedbaser

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 bedbaser version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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