R Observatory: Metrics for InteractionSet version 1.40.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

InteractionSet

Bioc current

Base Classes for Storing Genomic Interaction Data

v1.40.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.3 · May 4, 2016

Current · Requires R 4.6

1.0 In 21 of 49 releases 3.23

Description

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

86 1 exported

Complexity

3 avg / 10 max

Call network

86 nodes / 43 edges

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

Call graph

Open call graph →

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Lowest coverage

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

Code

Structure

Lines of code

9,463

Files

64

Compiled share

9.1%

Has compiled src

Yes

Language breakdown

R 2,320 (24.5%)C/C++/src 859 (9.1%)Tests 2,829 (29.9%)Docs 2,599 (27.5%)Vignettes 856 (9%)

API

Exported functions

1

Internal functions

34

Testing & CI

Has tests

Yes

Test-to-code ratio

1.22

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

11.1%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

1

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

21

First release

2016-06-14

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

3

LOC over versions

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

Documentation

READMEYes · 47 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Topics

Software › Infrastructure

Software › Infrastructure › DataRepresentation

Software

Software › Technology › Sequencing › HiC

Depended on by (40)

CRAN (3)

hicream treediff CNVScope

People

Aaron Lun author maintainer
Elizabeth Ing-Simmons author
Malcolm Perry author

At a glance

Version: 1.40.0
Category: software
License: GPL-3
Requires R: ≥ 4.6
Maintainer: Aaron Lun
Entered: 3.3 · May 4, 2016
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

GenomicRangesBiocSummarizedExperimentBioc

Imports

methodsMatrix RcppBiocGenericsBiocS4Vectors (>= 0.27.12)BiocIRangesBiocSeqinfoBioc

Suggests

testthat knitr rmarkdownBiocStyleBioc

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("InteractionSet")

Format

Lun, A., Ing-Simmons, E., & Perry, M. (2026). InteractionSet: Base Classes for Storing Genomic Interaction Data (Version 1.40.0) [Computer software]. https://bioconductor.org/packages/InteractionSet

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 InteractionSet version 1.40.0 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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