HicAggR
Bioc currentSet of 3D genomic interaction analysis tools
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
69 33 exported
Complexity
7.7 avg / 47 max
Call network
69 nodes / 118 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
12,507
Files
98
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
33
Internal functions
35
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
3
Docs
Roxygen coverage
97%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
15
Dep constraint coverage
0%
Secret pattern count
0
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
5
First release
2024-05-10
Latest release
2026-04-28
Avg cadence
177 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
- 42 (6 internal)includes a package overview page
- Examples that run
- 100%37 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/cuvierlab/hicaggr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2024-07-07 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Beaf32_Peaks.gnr | – | – | – |
| HiC_Ctrl.cmx_lst | list | 3 elements | No other package |
| HiC_HS.cmx_lst | list | 3 elements | No other package |
| TADs_Domains.gnr | – | – | – |
| TSS_Peaks.gnr | – | – | – |
Topics
People
- Olivier Cuvier maintainer contributor
- Refka Askri contributor
- Nicolas Chanard author
- David Depierre author
- Pascal Martin contributor
- Stéphane Schaak author contributor
- Naomi Schickele contributor
- Robel Tesfaye author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HicAggR")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.