R3CPET
Bioc current3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
109 4 exported
Complexity
4.4 avg / 19 max
Call network
109 nodes / 36 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
6,181
Files
95
Compiled share
20%
Has compiled src
Yes
Language breakdown
API
Exported functions
4
Internal functions
50
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
23
First release
2015-04-16
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 35includes a package overview page
- Examples that run
- 91%31 run in a plain check · 3 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 46%
Repository practices
Checks run against github.com/sirusb/r3cpet on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Chromosoms | data.frame | 24 × 2 | No other package |
| PPI.Biogrid | igraph | 169,166 edges | No other package |
| PPI.HPRD | igraph | 39,042 edges | No other package |
| RPKMS | data.frame | 30,627 × 2 | No other package |
| geneLocations.nucleus | data.frame | 5,736 × 11 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("R3CPET")The package provides a citation file, so citation() returns the authors' own entry.
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.