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I wonder if it would be better to just use something like DEseq2 beforehand, to aggregate replicates. But I may be wrong. Just making sure we're not reinventing the wheel if there's another package that takes care of every corner case. It would be nice to keep all in one Python pipeline, though...
We have something else that we're developing in our lab that will be used as a separate tool for this issue. I will post is here and close the issue when it's released.
It would be easy enough to add a feature to handle replicates in the process_atac side of things... probably something to consider in the near future.
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