R Observatory: Metrics for plyinteractions version 1.10.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

plyinteractions

Bioc current

Extending tidy verbs to genomic interactions

v1.10.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.18 · Oct 25, 2023

Current · Requires R 4.6

1.0 In 6 of 49 releases 3.23

Description

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

118 17 exported

Complexity

1.8 avg / 10 max

Call network

118 nodes / 50 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

8,436

Files

103

Compiled share

0%

Has compiled src

No

Language breakdown

R 4,142 (49.1%)Tests 1,150 (13.6%)Docs 2,258 (26.8%)Vignettes 886 (10.5%)

API

Exported functions

38

Internal functions

101

Recent export changes

v3.22−36 anchor, anchor_3p, anchor_5p 33 more

v3.20+4 add_pairdist, pair_granges, write_bedpe +1 more

Testing

Has tests

Yes

Test-to-code ratio

0.28

testthat edition

3

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

6

First release

2023-10-24

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

2

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 · 499 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structuredCitation fileNo

Help pages: 31 (3 internal)includes a package overview page
Examples that run: 100%27 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

plyinteractions HTML
HiCarithmetic HTML

How these are measured

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/js2264/plyinteractions on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-05

Coverage (1)

Coverage reporting (Codecov)

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

Datasets

Bundled datasets · 3

Name	Class	Size	Also in
GM12878_HiCCUPS	–	–	–
ce10_ARCC	–	–	–
ce10_REs	–	–	–

All of plyinteractions's data objects

Topics

Software

Software › Infrastructure

Maintainer: Jacques Serizay

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (2)

Bioconductor (2)

GenomicCoordinates OHCA

Suggested by (1)

tidyomics

People

Jacques Serizay author maintainer

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("plyinteractions")

Format

Serizay, J. (2026). plyinteractions: Extending tidy verbs to genomic interactions (Version 1.10.0) [Computer software]. https://bioconductor.org/packages/plyinteractions

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 plyinteractions version 1.10.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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