GenomicInteractions
Bioc currentUtilities for handling genomic interaction data
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 15 exported
Complexity
3 avg / 14 max
Call network
30 nodes / 16 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
5,654
Files
87
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
44
Internal functions
15
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
13.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-10-28
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 48includes a package overview page
- Examples that run
- 100%29 run in a plain check
- Exported functions with examples
- 87%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 4%
Repository practices
Checks run against github.com/computationalregulatorygenomicsicl/genomicinteractions on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Seitan2013_WT_100kb_interactions | data.frame | 23,276 × 20 | No other package |
| hg19.refseq.transcripts | – | – | – |
| hic_example_data | – | – | – |
| k562.rep1.cluster.pet3+ | data.frame | 64,565 × 9 | No other package |
| mm9_refseq_promoters | – | – | – |
| thymus_enh | – | – | – |
Topics
Depended on by (5)
People (from the free-text Author field)
- Harmston
- N.
- Ing-Simmons
- E.
- Perry
- M.
- Baresic
- A.
- Lenhard
- B.
Cite
Cite this package
Run in R for the authors' entry:
citation("GenomicInteractions")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12864-015-2140-x.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.