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Dear all,
would you please let me know which BioC packages would you recommend for computing the enrichment in ChIP-seq or CUT-RUN experiments in order to show that the quality of the peaks in one experiment 1 is much better than the quality/intensity of the peaks in another experiment 2 ? (BioC packages beside ChIPQC and SPP). Thanks,
~ Bogdan
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Have you tried
phantompeakqualtools
?Not directly. I have inspected the PhantomPeak that was provided by ChIPQC.