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 (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/CorNetto
git_branch: devel
git_last_commit: 20ca097
git_last_commit_date: 2026-08-25
Repository: Bioconductor 3.24
Date/Publication: 2026-09-14
NeedsCompilation: no
Packaged: 2026-09-14 21:06:28 UTC; biocbuild
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>
