CEMiTool 
A modified version of the Co-Expression Module Identification Tool (CEMiTool) (modified by Brett Chapman)
Docker Image
For more information about using the official CEMiTool Docker image, see here The Dockerfile has been modified by Brett Chapman to utilise this GitHub repo
Updates to this version of CEMiTool
New parameters have been added to the CEMiTool.R executable in exec/ and the script has been significantly updated with added functionality.
In addition the Beta value can now be set manually or forced if R squared is below 0.8, as explained in point 6 here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html.
Usage:
--top_hubs N (default: 10) to output a list of the top N hub genes per module, and a filtered expression matrix is also output for use in other tools if desired.
--top_hubs_interact N (default: 10) to use the top N hub genes as the basis of the interaction network.
--set-beta N (default: 'None') set the Beta value manually.
--force-beta N (default: 'None') force the Beta value if R squared is found to be below 0.8.
Another parameter included which was left out from the original executable is --cor-function=<corfunc>
A python script has also been included which converts GFF to a GMT file if wanting to generate a gene set for ORA analysis. Modification of the python script may be nessary depending on the formatting of your GFF file. A test.gff file has been included in tests/.
Please use this version of CEMiTool if you would like to run CEMiTool on a cluster with the executable through Docker or Singularity instead of RStudio, and if you would like to see a list of the top hub genes, use these genes for the interaction network (if you don't have a interactome of your own), and would like to slice the original expression matrix by hub genes and transformed using VST.