I have an time-course RNA-seq data set with 8 different time points. I am trying to find expression patterns in the data - clusters of genes that change in similar ways throughout the experimental conditions.
I guess one option would be to do pair-wise comparisons in DESeq2 by specifying the contrast. But since I am not interested in comparing only two of the time points, I was looking for an alternative that would allow me to consider expression patterns in the whole data set. I have found the FunPat package, but cannot seem to get this to work.
I would appreciate any advice since I am not sure how to proceed. Does anyone have experience with this kind of analysis and can recommend a good package or function that I should look into?