Basic4Cseq
Bioc currentBasic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 0 exported
Complexity
3.7 avg / 32 max
Call network
36 nodes / 0 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
2,988
Files
65
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
36
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
–
C++ standard
–
License
LGPL-3
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-06-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22
- Examples that run
- 100%22 run in a plain check (8 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 23%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RCircos_GRCm38_ideogram | data.frame | 403 × 5 | No other package |
| RCircos_HG19_ideogram | data.frame | 862 × 5 | No other package |
| enzymeData | data.frame | 7 × 2 | No other package |
| fetalLiver_finalFragments | data.frame | 284 × 4 | No other package |
| liverData | – | – | – |
| liverDataRaw | – | – | – |
| transInteractionData | data.frame | 4 × 4 | No other package |
| veryShortLib | data.frame | 1 × 10 | No other package |
| vfl_aagctt_catg_mm9_54_vp | data.frame | 453 × 10 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Basic4Cseq")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.