Hi, I have treatment-control time course RNA-seq data. I have 7 time points for both control and treatment. Currently, I already use edgeR to identify the differentially expressed genes considering the RNA-seq data as time course data.
I got around 2000 DE genes. Then I'd like to construct co-express network to classify these DE genes for functional analysis. The problem is I have two time courses. How should I treat the data when constructing the co-expression gene? Or what methods or tools should I use for such datasets? Thanks.