crupR
Bioc currentAn R package to predict condition-specific enhancers from ChIP-seq data
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
An R package that offers a workflow to predict condition-specific enhancers from ChIP-seq data. The prediction of regulatory units is done in four main steps: Step 1 - the normalization of the ChIP-seq counts. Step 2 - the prediction of active enhancers binwise on the whole genome. Step 3 - the condition-specific clustering of the putative active enhancers. Step 4 - the detection of possible target genes of the condition-specific clusters using RNA-seq counts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
26 7 exported
Complexity
5.7 avg / 32 max
Call network
26 nodes / 17 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
2,678
Files
62
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
19
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.27
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
4.4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-04-15
Latest release
2026-04-28
Avg cadence
189 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
- Help pages
- 8includes a package overview page
- Examples that run
- 86%6 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 13%
- crupR Vignette HTML
Repository practices
Checks run against github.com/akbariomgba/crupr on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RegulatoryUnits | – | – | – |
| RegulatoryUnitsNearestGene | – | – | – |
| active_vs_inactive | randomForest.formula | 14 elements | No other package |
| condition1_predictions | – | – | – |
| condition2_clusters | – | – | – |
| condition2_inputfree_normalized | – | – | – |
| condition2_normalized | – | – | – |
| condition2_peaks | – | – | – |
| condition2_predictions | – | – | – |
| differential_enhancers | – | – | – |
| ecdf | list | 7 elements | No other package |
| enhancer_vs_active_promoter | randomForest.formula | 14 elements | No other package |
| expressions | – | – | – |
Topics
Depended on by (1)
Bioconductor (1)
People
- Persia Akbari Omgba maintainer
- Verena Laupert author
- Martin Vingron author
Cite
Cite this package
Run in R for the authors' entry:
citation("crupR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-019-1860-7.
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.