DESCRIPTION

Package: GWENA
Title: Pipeline for augmented co-expression analysis
Version: 1.11.0
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