scWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in single-cell RNA-seq data. scWGCNA constructs co-expression networks in a cell-type-specific manner, identifies robust modules of highly inerconnected genes, and provides biological context for these modules. For ease of use, scWGCNA is directly compatible with Seurat objects, one of the most common formats for single-cell data.
We recommend creating an R conda environment environment for scWGCNA.
conda create -n scWGCNA -c conda-forge r-base r-essentials
install.packages('WGCNA')
install.packages('igraph')
install.packages('devtools')
# install Seurat, check their website for the most up-to-date instructions
install.packages('Seurat')
Now you can install the scWGCNA package using devtools:
devtools::install_github('smorabit/scWGCNA')