HiCExperiment
Bioc currentBioconductor class for interacting with Hi-C files in R
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
65 12 exported
Complexity
3.5 avg / 20 max
Call network
65 nodes / 123 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
7,091
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
52
Testing
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
182 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
- Help pages
- 21 (9 internal)
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 89%
- Documented parameters
- 63%
- Return-value docs
- 22%
- Help pages citing references
- 0%
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/js2264/hicexperiment on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-05
Datasets
Topics
Depended on by (6)
Bioconductor (6)
People
- Jacques Serizay author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("HiCExperiment")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41467-024-44761-x.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.