R Observatory: Metrics for HiCParser version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HiCParser

Bioc current

Parser for HiC data in R

v1.4.0 · software · LGPL

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

This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

34 5 exported

Complexity

3.6 avg / 12 max

Call network

34 nodes / 45 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

2,390

Files

51

Compiled share

22.1%

Has compiled src

Yes

Language breakdown

R 943 (39.5%)C/C++/src 527 (22.1%)Tests 280 (11.7%)Docs 277 (11.6%)Vignettes 363 (15.2%)

API

Exported functions

5

Internal functions

11

Recent export changes

v3.21+5 mergeInteractionSet, parseCool, parseHiC +2 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.30

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

10%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

LGPL

License flags

not SPDX, not OSI

History

Versions

3

First release

2025-04-15

Latest release

2026-04-28

Avg cadence

189 days

Cold removal rate

–

Dep drift

2

LOC over versions

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

Documentation

READMEYes · 747 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductYesContributing guideYes

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

Topics

Software

Software › Technology › Sequencing › HiC

Software › Infrastructure › DataImport

Depended on by (1)

CRAN (1)

treediff

People

Maigné Élise author maintainer
Zytnicki Matthias author

At a glance

Version: 1.4.0
Category: software
License: LGPL
Requires R: ≥ 4.6
Maintainer: Maigné Élise
Entered: 3.21 · Apr 16, 2025
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Imports

data.tableInteractionSetBiocGenomicRangesBiocSummarizedExperimentBiocRcpp (>= 1.0.12)S4VectorsBiocgtools pbapplyBiocGenericsBiocSeqinfoBioc

Suggests

rhdf5BiocBiocStyleBiocknitr sessioninfo testthat (>= 3.0.0)

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HiCParser")

Format

Élise, M., & Matthias, Z. (2026). HiCParser: Parser for HiC data in R (Version 1.4.0) [Computer software]. https://bioconductor.org/packages/HiCParser

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 HiCParser version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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