Wondering if anyone could give a bit of advice on my situation. I have rnqseq ngs data for 6 different human cell lines. Each has a normal and a stressed condition. I have featurecounts for each of those that are the summation of the replicates, so 12 summary count files. I have successfully compared each matching line stressed-normal but was wondering if there was a simple way to visualize possible significant genes when comparing each line to another (eg: instead of just Line1 stressed vs Line1 normal, I could easily plot all of the top 20 or so genes of significance by logFC and visualize overlaps that may exist between Line1 normal and any of the other lines, Line1 normal to Line3 normal. One large multi-colored plot type? Instead of running limma on each possible comparison (66 possible pairwise comparisons, which would be a crazy amount of data to then manually try to find overlaps within).
We are looking for some very early preliminary hints as to comparisons between these lines with regard to up and down regulated similarities. Would obviously dig into individual comparisons in a different way after but was hoping to some sort of visualization plot method without having to run each comparison individually and then seeking out common top genes that overlap. Hope that makes sense. Tried to solve this for myself prior to asking here.