R Observatory: Metrics for plyranges version 1.32.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

plyranges

Bioc current

A fluent interface for manipulating GenomicRanges

v1.32.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.7 · May 1, 2018

Current · Requires R 4.6

1.0 In 17 of 49 releases 3.23

Description

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

415 124 exported

Complexity

1.5 avg / 9 max

Call network

415 nodes / 287 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.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

12,584

Files

150

Compiled share

0%

Has compiled src

No

Language breakdown

R 6,091 (48.4%)Tests 2,816 (22.4%)Docs 3,086 (24.5%)Vignettes 591 (4.7%)

API

Exported functions

130

Internal functions

290

Recent export changes

v3.9+1 expand_ranges −1 unnest

v3.8+3 !!!, !!, n_distinct −4 UQ, UQS, enquo 1 more

Testing

Has tests

Yes

Test-to-code ratio

0.46

testthat edition

–

Docs

Roxygen coverage

96.9%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

35.7%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

17

First release

2018-06-06

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

3

LOC over versions

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

Documentation

In the Bioconductor 3.23 release

READMEYes · 437 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.32.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 54 (1 internal)includes a package overview page
Examples that run: 94%44 run in a plain check · 3 never run
Exported functions with examples: 91%
Documented parameters: 78%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

Introduction HTML
Additional examples of plyranges HTML

Changes in 1.32.0 (Bioconductor 3.23)

added new functionality for slice_*, as in dplyr, including head, tail, max, min and sample. These include the dplyr arguments such as n, prop, and weight_by (for sampling).
added join_mcols_left(x,y) for GRanges x and tabular y
added distance=TRUE option for join_overlap_*

From NEWS.md in the release

How these are measured

Repository practices

Upstream repositoryBeta

10 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/tidyomics/plyranges on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux and macOS

Governance and community (3)

Code of conductContributing guideIssue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-30 · The repository has a site deploy workflow

pkgdown site last built 2026-07-30

Coverage (1)

Coverage reporting

Show all practicesHide 1 practice

Reproducibility and dev environment (1)

Makefile

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

Topics

Software › Infrastructure

Software › Infrastructure › DataRepresentation

Software › WorkflowStep

Software › BiologicalQuestion › Coverage

Maintainer: Michael Love

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (27)

Show all 38 packagesHide all 38 packages

Suggested by (11)

dbSequence EpiCompare extraChIPs memes NUMTDetect rigvf RTDetect savingBiocObjects svaNUMT svaRetro tidyCoverage

People

Michael Love contributor maintainer
Pierre-Paul Axisa contributor
Dianne Cook author contributor
Michael Lawrence author contributor
Stuart Lee author
Spencer Nystrom contributor

Cite

Cite this package

Run in R for the authors' entry:

citation("plyranges")

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

It points to 10.1186/s13059-018-1597-8.

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 plyranges version 1.32.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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