Package: CorNetto
Title: Knowledge-Guided Multi-Omic Correlation Network Analysis
Version: 0.99.1
Authors@R: c(
    person("Bradley", "Ward", role = c("aut", "cre"),
           email = "bradleyalexward@gmail.com",
           comment = c(ORCID = "0000-0003-0778-0153")),
    person("Jean-Luc", "Balligand", role = "ctb"),
    person("Laurence", "Bamps", role = "ctb"),
    person("Patrice D.", "Cani", role = "ctb"),
    person("Julien", "De Greef", role = "ctb"),
    person("Joseph P.", "Dewulf", role = "ctb"),
    person("Vincent", "Haufroid", role = "ctb"),
    person("Benoît", "Kabamba", role = "ctb"),
    person("Sébastien", "Pyr dit Ruys", role = "ctb"),
    person("Didier", "Vertommen", role = "ctb"),
    person("Jean Cyr", "Yombi", role = "ctb"),
    person("Leïla", "Belkhir", role = c("ths", "fnd"),
           email = "leila.belkhir@saintluc.uclouvain.be"),
    person("Laure", "Elens", role = c("ths", "fnd"),
           email = "laure.elens@uclouvain.be"),
    person("Sofina COVID Solidarity Fund", role = "fnd")
    )
Description: Builds knowledge-guided multi-omic correlation networks
        from normalized transcriptomic, proteomic, and metabolomic
        abundance data. Group-specific correlation networks are
        compared with the Fisher z-difference test, either across all
        within-omic pairs in one or every assay without generating
        cross-omic pairs, or across candidate edges supplied by a
        prior-knowledge network, and the resulting differential network
        is summarized into node-level rewiring scores that identify
        features whose interaction patterns change between groups.
        Rewiring scores can be compared with group-label permutation
        reference distributions, and networks can be restricted to
        pathway-focused neighbourhoods, converted to 'igraph' objects,
        or exported as Cytoscape-ready node and edge tables. The
        package is built on Bioconductor containers so that multi-omic
        assays and sample metadata are managed consistently throughout
        the workflow.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: BiocParallel, graphics, igraph, methods, MultiAssayExperiment,
        S4Vectors, stats, SummarizedExperiment, tools, utils, withr
Suggests: BiocManager, BiocStyle, knitr, qvalue, rmarkdown, testthat
        (>= 3.0.0)
VignetteBuilder: knitr
biocViews: GraphAndNetwork, Metabolomics, Network, NetworkInference,
        Proteomics, SystemsBiology, Transcriptomics
URL: https://github.com/bradleyalexward/CorNetto
BugReports: https://github.com/bradleyalexward/CorNetto/issues
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-25 08:48:58 UTC
RemoteUrl: https://github.com/bioc/CorNetto
RemoteRef: HEAD
RemoteSha: 20ca097f7480bb0dfc0c6f56f6ac16aaccc089af
NeedsCompilation: no
Packaged: 2026-10-16 10:50:50 UTC; root
Author: Bradley Ward [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0778-0153>),
  Jean-Luc Balligand [ctb],
  Laurence Bamps [ctb],
  Patrice D. Cani [ctb],
  Julien De Greef [ctb],
  Joseph P. Dewulf [ctb],
  Vincent Haufroid [ctb],
  Benoît Kabamba [ctb],
  Sébastien Pyr dit Ruys [ctb],
  Didier Vertommen [ctb],
  Jean Cyr Yombi [ctb],
  Leïla Belkhir [ths, fnd],
  Laure Elens [ths, fnd],
  Sofina COVID Solidarity Fund [fnd]
Maintainer: Bradley Ward <bradleyalexward@gmail.com>