I was wondering if there a way to run a time series analysis on ChIP-Seq data. We have duplicates of four different time points for two strains and three conditions. We have done IP, Input and IgG samples. Now I would like to identify differences over time comparing the different conditions w.o. the need of doing multiple pair-wise comparisons.
I couldn't find any tool for that. Is it possible to take the same tools as for RNA-Seq samples? (by that I mean - DESeq2, edgeR, limma-voom etc.)