sevenC
Bioc currentComputational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
15 11 exported
Complexity
1.9 avg / 7 max
Call network
15 nodes / 8 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
3,579
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.54
testthat edition
–
CI present
Yes
CI type
["github-actions","travis"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
91.7%
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
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 4%
Topics
People
- Jonas Ibn-Salem author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("sevenC")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.