You are going to want to work with the WGNCA package in R, produced by Peter Langfelder and Steve Horvath.

The overview of how the program works is described here: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/index.html

and here:

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Simulated-00-Background.pdf

Full R scripts/demos are available here on their website:

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html

Your question about the data input format can be found here:

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-01-dataInput.pdf