I am working on a genome-wide study and struggling with gene co-expression network analysis. I am working on Tomato(Solanum lycopersicum). Can someone suggest me some tools or methods for this analysis? Currently, I am trying to use the ATTED II tool for this but I am not sure that the results will be good enough.
I tried to use RNA seq data and WebChemitool but there is some kind of error and I couldn't find any way to solve the problem. Please can someone tell me what can I do now?