I am new here and I have a question for you guys: which is the best tool to predict if a specific list of genes is up- or downregulated in your RNA-SEQ data? I am trying GSEA but I was wondering if there are better tools available.
I used DEseq, but what I need is: I created my personal list of genes of interest and I was wondering if there is a way to verify if these genes are up- or down regulated not as single but as group. (I have 4 samples each in triplicates). Thanks