Package: DNEA
Title: Differential Network Enrichment Analysis for Biological Data
Version: 1.0.0
Authors@R: c(
      person(given = "Christopher", family = "Patsalis", 
             email = "chrispatsalis@gmail.com", role = c("cre", "aut"),
             comment = c(ORCID = "0009-0003-4585-0017")),
      person(given = "Gayatri", family = "Iyer", 
             email = "griyer@umich.edu", role = c("aut")),
             person(given = "Alla", family = "Karnovsky", 
             email = "akarnovs@med.umich.edu", role = c("fnd"),
             comment = c(NIH_GRANT = "1U01CA235487")),
             person(given = "George", family = "Michailidis", 
             email = "gmichail@ufl.edu", role = c("fnd"),
             comment = c(NIH_GRANT = "1U01CA235487")))
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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
output: BiocStyle::html_document vignette: >
        %\VignetteIndexEntry{Vignette Title}
        %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}
        ---
Imports: BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3),
        janitor, Matrix, methods, netgsa, stats, stringr, utils,
        SummarizedExperiment
Collate: 'JSEM-internals.R' 'aggregate-features.R' 'all-classes.R'
        'all-generics.R' 'all-methods.R' 'clustering-internals.R'
        'initiator.R' 'start-here.R' 'utilities-internals.R'
        'utilities-exported.R' 'primary.R'
Depends: R (>= 4.2)
LazyData: false
Suggests: BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap,
        rmarkdown, testthat (>= 3.0.0), withr, airway
Enhances: massdataset
URL: https://github.com/Karnovsky-Lab/DNEA
BugReports: https://github.com/Karnovsky-Lab/DNEA/issues
biocViews: Metabolomics, Proteomics, Lipidomics,
        DifferentialExpression, NetworkEnrichment, Network, Clustering,
        DataImport
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 libzmq3-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:36:34 UTC
RemoteUrl: https://github.com/bioc/DNEA
RemoteRef: RELEASE_3_22
RemoteSha: a831e55a59602a5521c8a6f1ee0f84347d7f6918
NeedsCompilation: no
Packaged: 2026-03-03 09:07:01 UTC; root
Author: Christopher Patsalis [cre, aut] (ORCID:
    <https://orcid.org/0009-0003-4585-0017>),
  Gayatri Iyer [aut],
  Alla Karnovsky [fnd] (NIH_GRANT: 1U01CA235487),
  George Michailidis [fnd] (NIH_GRANT: 1U01CA235487)
Maintainer: Christopher Patsalis <chrispatsalis@gmail.com>
Built: R 4.5.2; ; 2026-03-03 09:09:34 UTC; windows
