HiCParser
Bioc currentParser for HiC data in R
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
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.
None published for Bioconductor
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 →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,388
Files
38
Compiled share
22.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
5
Internal functions
11
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
3
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
- Help pages
- 6includes a package overview page
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
11 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/emaigne/hicparser on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2026-07-07 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| hicsample_21 | data.frame | 44 × 4 | No other package |
Topics
Depended on by (1)
CRAN (1)
People
- Maigné Élise author maintainer
- Zytnicki Matthias author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HiCParser")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.