DNEA
This is the development version of DNEA; for the stable release version, see DNEA.
All Bioconductor versions of DNEA
3.24 (devel), 3.23 (release), 3.22
Differential Network Enrichment Analysis for Biological Data
Bioconductor version: 3.24 · Package version: 1.3.0
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.
Author: Christopher Patsalis [cre, aut] 
, Gayatri Iyer [aut], Alla Karnovsky [fnd] (NIH_GRANT: 1U01CA235487), George Michailidis [fnd] (NIH_GRANT: 1U01CA235487)
Maintainer: Christopher Patsalis <chrispatsalis at gmail.com>
Citation
From within R, enter citation("DNEA"):
Christopher Patsalis, Gayatri Iyer. DNEA: Differential Network Enrichment Analysis for Biological Data. doi:10.18129/B9.bioc.DNEA, R package version 1.3.0, https://bioconductor.org/packages/DNEA.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DNEA")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.3.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/Karnovsky-Lab/DNEA |
| Bug Reports | https://github.com/Karnovsky-Lab/DNEA/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 2127 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, DifferentialExpression, Lipidomics, Metabolomics, Network, NetworkEnrichment, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/DNEA/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DNEA")| Differential Network Expression Analysis for Metabolomics Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | DNEA_1.3.0.tar.gz |
| Windows binary (x86_64) | DNEA_1.3.0.zip |
| macOS binary (arm64) | DNEA_1.3.0.tgz |
| macOS binary (x86_64) | DNEA_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DNEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DNEA |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.2)
Imports: BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3), janitor, Matrix, methods, netgsa, stats, stringr, utils, SummarizedExperiment
Suggests: BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway
Enhances: massdataset