Code to reproduce WGCNA for BMI brain project

How to run

1. clone the repo
2. download the expression data #TODO
3. install the required R packages
   1. Install Seurat 2.3.3 by following the instructions here or downloading the source from github and installing from within an R session using install.packages(pkgs="<path_to_seurat_source>", type=source, repos=NULL)
   2. Install Bioconductor packages Biobase and STRINGdb
   3. Install CRAN packages by installing renv and running either renv::init() or renv::restore(lockfile="./renv.lock"). Alternatively install the packages manually: here, optparse, dplyr, Matrix, parallel, reshape, reshape2, liger, boot, R.utils, readr. For a full list of packages loaded into the session namespace, see packages.txt
4. Edit the parameters in run_wgcna.sh as desired (run Rscript ./wgcna.R --help for information on parameters) and run the analysis using bash run_wgcna.sh