igor

Thank you for looking into it. It's reassuring to know that there is not a clear standard, so neither option is "wrong". However, org.\*.db and TxDb.\* packages are probably more...

Curiously, I've seen some packages add specific workarounds related to ggplot2 3.5, so it's definitely a widespread issue without a simple elegant fix. For example, hrbrthemes (with over 1k GitHub...

I will give it a try. I can also share the input matrix if you'd like. Regarding subsampling, I was using the same input matrix for both versions.

The differences are variable. For example, 4,000 to 5,400, 2,600 to 2,100, 3,100 to 8,100. Obviously, these are not very good samples, so that may have something to do with...

I saw that, but wasn't sure how to properly use the output to determine the optimal values. Do you have an example documented somewhere?

I am sharing the cutoff report here (I had to add .txt because curiously GitHub does not allow .tsv): [test_cutoff_analysis.tsv.txt](https://github.com/macs3-project/MACS/files/14912573/test_cutoff_analysis.tsv.txt) It might even be easier to just paste it in...

> Not a direct answer, but the scale on your IGV is quite different as well between the two Yes, each sample is auto-scaled independently since peak-calling is independent as...

I am not surprised that machine learning is failing for these samples. I was primarily concerned about the large difference between the Java and MACS3 implementations.

It might be helpful to include this warning in the README and/or DESCRIPTION files. I suspect many users may not check the issues section, which may explain why packages continue...

This was almost 8 years ago (just one week off). I don't remember all the details. I have not used `bedtools annotate` since then. I don't see anything mentioned in...