I am using Diffbind to compare H3K27ac peaks between two time points. Recently, we added 4 more time points to the existing 2 to do time-series comparison. From my understanding, Diffbind could conventionally compare and provide differential bound sites between 2 samples .
Q1: Is there a way to compare and contrast 6 time-points, considering each has 2 biological replicates. Q2 If the answer to Q1 is no, when I compare A to B and separately A to C , why do I get different counts for A in the binding affinity matrix arising from A vs B to A vs C for the same peak interval.