Package: GWENA
Title: Pipeline for augmented co-expression analysis
Version: 1.21.0
Authors@R: 
    c(person(given = "Gwenaëlle",
             family = "Lemoine",
             role = c("aut", "cre"),
             email = "lemoine.gwenaelle@gmail.com",
             comment = c(ORCID = "0000-0003-4747-1937")),
      person(given = "Marie-Pier",
             family = "Scott-Boyer",
             role = "ths"),
      person(given = "Arnaud",
             family = "Droit",
             role = "fnd"))
Description: The development of high-throughput sequencing led to
        increased use of co-expression analysis to go beyong single
        feature (i.e. gene) focus. We propose GWENA (Gene Whole
        co-Expression Network Analysis) , a tool designed to perform
        gene co-expression network analysis and explore the results in
        a single pipeline. It includes functional enrichment of modules
        of co-expressed genes, phenotypcal association, topological
        analysis and comparison of networks configuration between
        conditions.
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.1.1
Depends: R (>= 4.1)
Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16),
        prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1),
        BiocStyle (>= 2.15.8)
Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1),
        ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5),
        tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph
        (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist
        (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>=
        1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>=
        4.0.4), methods, graphics, stats, utils
VignetteBuilder: knitr
biocViews: Software, GeneExpression, Network, Clustering,
        GraphAndNetwork, GeneSetEnrichment, Pathways, Visualization,
        RNASeq, Transcriptomics, mRNAMicroarray, Microarray,
        NetworkEnrichment, Sequencing, GO
BugReports: https://github.com/Kumquatum/GWENA/issues
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:00:28 UTC
RemoteUrl: https://github.com/bioc/GWENA
RemoteRef: HEAD
RemoteSha: 28d0013286c97fe4be4358d11f666e82d1befa7b
NeedsCompilation: no
Packaged: 2025-11-23 13:17:28 UTC; root
Author: Gwenaëlle Lemoine [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4747-1937>),
  Marie-Pier Scott-Boyer [ths],
  Arnaud Droit [fnd]
Maintainer: Gwenaëlle Lemoine <lemoine.gwenaelle@gmail.com>
Built: R 4.6.0; ; 2025-11-23 13:20:03 UTC; windows
