epiregulon
Bioc currentGene regulatory network inference from single cell epigenomic data
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
56 11 exported
Complexity
5 avg / 27 max
Call network
56 nodes / 58 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
6,291
Files
53
Compiled share
8.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
11
Internal functions
35
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.59
testthat edition
3
Docs
Roxygen coverage
100%
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
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-06-06
Latest release
2026-04-28
Avg cadence
157 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12 (1 internal)includes a package overview page
- Examples that run
- 100%10 run in a plain check
- Exported functions with examples
- 91%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 8%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/xiaosaiyao/epiregulon on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Suggested by (1)
People
- Xiaosai Yao author maintainer
- Shang-Yang Chen author
- Aaron Lun author
- Tomasz Włodarczyk author
Cite
Cite this package
Run in R for the authors' entry:
citation("epiregulon")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41467-025-62252-5.
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.