DNEA
Bioc currentDifferential Network Enrichment Analysis for Biological Data
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
The DNEA R package is the latest implementation of the Differential Network Enrichment Analysis algorithm and is the successor to the Filigree Java-application described in Iyer et al. (2020). The package is designed to take as input an m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) and jointly estimate the biological network associations of each condition using the DNEA algorithm described in Ma et al. (2019). This approach provides a framework for data-driven enrichment analysis across two experimental conditions that utilizes the underlying correlation structure of the data to determine feature-feature interactions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
93 12 exported
Complexity
3.4 avg / 16 max
Call network
93 nodes / 47 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
10,481
Files
87
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
35
Internal functions
81
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 46includes a package overview page
- Examples that run
- 100%40 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 17%
- DNEA HTML
Repository practices
Checks run against github.com/karnovsky-lab/dnea on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| T1Dmeta | data.frame | 322 × 7 | No other package |
| TEDDY | matrix | 134 × 322 | No other package |
| dnw | – | – | – |
| metab_data | data.frame | 134 × 3 | No other package |
Topics
People
- Christopher Patsalis maintainer author
- Gayatri Iyer author
-
Alla Karnovsky
funder
1U01CA235487
-
George Michailidis
funder
1U01CA235487
Cite
Cite this package
Run in R for the authors' entry:
citation("DNEA")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-024-05994-1.
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.