CexoR
Bioc currentAn R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4 2 exported
Complexity
17.5 avg / 50 max
Call network
4 nodes / 2 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
780
Files
22
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
0
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
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
Artistic-2.0 | GPL-2 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
26
First release
2013-10-14
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
- 4 (1 internal)includes a package overview page
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 75%
- CexoR Vignette PDF
Repository practices
Checks run against github.com/pmb59/cexor on 2026-10-25.
No development-tooling practices detected in the upstream repository.
Topics
People
- Pedro Madrigal author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("CexoR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.14806/ej.21.0.837.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.