HiCaptuRe
Bioc currentHiCaptuRe: Manipulating and integrating Capture Hi-C data
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
Capture Hi-C is a set of techniques that enable the detection of genomic interactions involving regions of interest, known as baits. By focusing on selected loci, these approaches reduce sequencing costs while maintaining high resolution at the level of restriction fragments. HiCaptuRe provides tools to import, annotate, manipulate, and export Capture Hi-C data. The package accounts for the specific structure of bait–otherEnd interactions, facilitates integration with other omics datasets, and enables comparison across samples and conditions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 10 exported
Complexity
3.5 avg / 21 max
Call network
36 nodes / 27 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
3,417
Files
54
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
26
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
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
4.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 16 (4 internal)includes a package overview page
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Functions HTML
- Introduction HTML
Repository practices
Checks run against github.com/lauretomas/hicapture on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| PAR_Homo_sapiens_coordinates | data.frame | 2 × 5 | No other package |
| annotation_example | data.frame | 1,052 × 5 | No other package |
Topics
People
- Laureano Tomas-Daza author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HiCaptuRe")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.