epiRomics
Bioc currentEpigenomic Analysis Package Built for R (epiRomics)
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
Integrates various levels of epigenomic information, including ChIP-seq, histone modification, ATAC-seq, and RNA-seq data. Regulatory network analysis uses combinatory approaches to infer regions of significance, such as enhancers. Downstream analysis identifies co-occurrence of epigenomic data at regions of interest. Visualization functions display multi-track genomic views with signal overlays. Please contact <ammawla@ucdavis.edu> for suggestions, feedback, or bug reporting.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
127 48 exported
Complexity
4.7 avg / 34 max
Call network
127 nodes / 147 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
16,202
Files
182
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
56
Internal functions
79
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.65
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
66.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 42 (1 internal)includes a package overview page
- Examples that run
- 100%40 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 97%
- Documented parameters
- 100%
- Return-value docs
- 97%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/huising-lab/epiromics on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-04-20 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example_epiRomics_BW_sheet | – | – | – |
| example_epiRomics_Db_sheet | data.frame | 15 × 5 | No other package |
| toy_database | – | – | – |
Topics
People
- Alex M. Mawla author maintainer
- Mark O. Huising author
Cite
Cite this package
Run in R for the authors' entry:
citation("epiRomics")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12864-023-09293-6, 10.1101/2021.08.19.456732.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.