Package: multiDEGGs
Title: Multi-Omic Differentially Expressed Gene-Gene Pairs
Version: 1.2.1.9000
Authors@R: 
    c(person(given = "Elisabetta",
          family = "Sciacca",
          role = c("aut", "cre", "cph"),
          email = "e.sciacca@qmul.ac.uk",
          comment = c(ORCID = "0000-0001-7525-1558")),
      person(given = "Myles",family = "Lewis",
          role = c("ctb"),
          email = "myles.lewis@qmul.ac.uk",
          comment = c(ORCID = "0000-0001-9365-5345")))
Maintainer: Elisabetta Sciacca <e.sciacca@qmul.ac.uk>
Description: Performs multi-omic differential network analysis by
        revealing differential interactions between molecular entities
        (genes, proteins, transcription factors, or other biomolecules)
        across the omic datasets provided. For each omic dataset, a
        differential network is constructed where links represent
        statistically significant differential interactions between
        entities. These networks are then integrated into a
        comprehensive visualization using distinct colors to
        distinguish interactions from different omic layers. This
        unified display allows interactive exploration of cross-omic
        patterns, such as differential interactions present at both
        transcript and protein levels. For each link, users can access
        differential statistical significance metrics (p values or
        adjusted p values, calculated via robust or traditional linear
        regression with interaction term) and differential regression
        plots. The methods implemented in this package are described in
        Sciacca et al. (2023) <doi:10.1093/bioinformatics/btad192>.
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: gzip
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Language: en-gb
URL: https://github.com/elisabettasciacca/multiDEGGs/,
        https://elisabettasciacca.github.io/multiDEGGs/
BugReports: https://github.com/elisabettasciacca/multiDEGGs/issues
Suggests: kernlab, nestedcv, pls, qvalue, randomForest, ranger,
        testthat (>= 3.0.0)
Imports: DT, grDevices, graphics, knitr, MASS, magrittr, methods,
        parallel, pbapply, pbmcapply, rmarkdown, sfsmisc, shiny,
        shinydashboard, stats, utils, visNetwork
Depends: R (>= 4.4.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libuv1-dev zlib1g-dev
Repository: https://elisabettasciacca.r-universe.dev
Date/Publication: 2026-06-16 12:07:41 UTC
RemoteUrl: https://github.com/elisabettasciacca/multideggs
RemoteRef: HEAD
RemoteSha: 6fa7a3d95f54b73ea35b59a81791bb11d8509d4f
NeedsCompilation: no
Packaged: 2026-06-16 12:50:01 UTC; root
Author: Elisabetta Sciacca [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-7525-1558>),
  Myles Lewis [ctb] (ORCID: <https://orcid.org/0000-0001-9365-5345>)