Package: GWENA
Title: Pipeline for augmented co-expression analysis
Version: 1.18.0
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
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: RELEASE_3_21
git_last_commit: 078fff0
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 01:13:03 UTC; biocbuild
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 4.5.0; ; 2025-04-16 14:37:51 UTC; windows
