mariner

Bioc current

Mariner: Explore the Hi-Cs

v1.12.0 · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.17 · Apr 26, 2023

Current · Requires R 4.6

1.0 In 7 of 49 releases 3.23

Description

Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

121 1 exported

Complexity

2.8 avg / 12 max

Call network

121 nodes / 93 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

19,540

Files

148

Compiled share

Has compiled src

Language breakdown

R 8,980 (46%)Tests 4,903 (25.1%)Docs 4,060 (20.8%)Vignettes 1,597 (8.2%)

API

Exported functions

Internal functions

118

Recent export changes

v3.22+13 InteractionJaggedArray, JaggedArray, aggMetadata +10 more −4 aggPairMcols, binPairs, getPairClusters 1 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.55

testthat edition

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

Dep constraint coverage

3.1%

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

First release

2023-04-25

Latest release

2026-04-28

Avg cadence

186 days

Cold removal rate

100%

Dep drift

LOC over versions

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

Documentation

READMEYes · 697 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideNo

Examples that run: 100%
Documented parameters: 90%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › FunctionalGenomics

Software › WorkflowStep › Visualization

Software › Technology › Sequencing › HiC

Depended on by (1)

Bioconductor (1)

nullranges

People

Eric Davis author maintainer
Sarah Parker author

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