DegCre
Bioc currentProbabilistic association of DEGs to CREs from differential data
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 17 exported
Complexity
3.6 avg / 15 max
Call network
31 nodes / 22 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
9,126
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
14
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
No
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
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
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
- Examples that run
- 55%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 3%
Topics
People
- Brian S. Roberts author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("DegCre")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.