installing_WGCNA_and_prereqs.txt

# installing prerequisites

install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival", "BiocManager")
BiocManager::install(c("GO.db", "preprocessCore", "impute"));

# the below code is for if you have an older version of R

# source("http://bioconductor.org/biocLite.R")
# biocLite(c("GO.db", "preprocessCore", "impute"))

# if you plan on using annotation capabilities (such as GOenrichmentAnalysis), then install the Bioconductor annotation packages

orgCodes = c("Hs", "Mm", "Rn", "Pf", "Sc", "Dm", "Bt", "Ce", "Cf", "Dr", "Gg");
orgExtensions = c(rep(".eg", 4), ".sgd", rep(".eg", 6));
packageNames = paste("org.", orgCodes, orgExtensions, ".db", sep="");

BiocManager::install(c("GO.db", "KEGG.db", "topGO", packageNames, "hgu133a.db", "hgu95av2.db", "annotate", "hgu133plus2.db", "SNPlocs.Hsapiens.dbSNP.20100427", "minet", "OrderedList"))

# install with CRAN

install.packages("WGCNA")

# install with bioconductor 

install.packages("BiocManager") 
BiocManager::install("WGCNA")

# install with GitHub

install.packages("devtools")
library(devtools)
install_github("cran/WGCNA")

# install with linux

$ wget https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/WGCNA_1.69-81.tar.gz
$ R CMD INSTALL WGCNA_1.69-81.tar.gz