GWENA (Gene Whole co-Expression Network Analysis) is an R package to perform gene co-expression network analysis in a single pipeline. This pipeline includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparisons of networks between conditions.
Using transcriptomics data from either RNA-seq or microarray, the package follows the steps displayed in Figure 1:
# Prerequisites
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
Installation can either be from:
BiocManager::install("GWENA")
# 2. From Bioconductor devel
BiocManager::install("GWENA", version = "devel")
# 3. From Github repository
BiocManager::install("Kumquatum/GWENA")
# OR
devtools::install_github("Kumquatum/GWENA")
A vignette is available at vignette/GWENA_guide.Rmd. To see the html version, use vignette("GWENA_guide")
.
Note: if you want to install from Github, please specify build_vignettes = TRUE
in install_github
.
GWENA is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License 3 (GPL 3) as published by the Free Software Foundation. It is distributed in the hope that it will be useful, but without any warranty and without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
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