Off topic:RNA-seq analysis: How to generate a master gene expression matrix to do co-expression cross all conditions of my samples

Question

[sclittlerain]

I am trying to perform gene co-expression analysis to identify the clusters of genes that co-express among all conditions of my samples (more than 2 conditions). To do that, I need to generate a master gene expression matrix that contain normalized counts or normalized FPKMs for each individual gene in all conditions. Could anyone guide me on the right way or the suitable bioinformatic packages that I can use to generate such master gene expression matrix? Thanks!