Danila

Hey @jnmark, thanks for raising it! While not an immediate solution to all of your questions, I'd just mention that we'll be working on synergies between squidpy and [muon](https://github.com/scverse/muon) for...

Hey @Raselel, thanks for reporting that. - And what the version of seaborn used here? Seems like it can't generate a histogram for the fragments in this region. - Are...

Thanks! Seaborn 0.11.1 seems to work for the PMBC10k and a few other datasets. I also tested the versions mentioned above in a clean environment (and `pysam=0.18.0`), and the following...

Hey @Raselel, to get back on this, I wasn't able to reproduce it on several scATAC-seq / multiome datasets. Was this issue resolved in any way? If not, should we...

Hey @gjhuizing, just wanted to say thank you! We're currently refactoring and rethinking the `atac` module, there will be more functionality to work with sequences in the near future, and...

There are at least these options to consider, I assume: - built-in Python `logging`, - scanpy `logging`, configurable through `scanpy.settings.verbosity`, - re-using scanpy `logging` internals but make it configurable through...

Thank you, @emdann! Thanks for raising this, we plan to improve how peak sequences are operated indeed. That should include GC content. Currently, there's [`ac.tl.get_sequences`](https://github.com/scverse/muon/blob/925fd904d20dd7b9c73c49591df8c032a60a5e09/muon/_atac/tools.py#L523) to get a list of...

Hey @PauBadiaM, Thanks for opening this issue, we've been moving away from `OrderedDict` in `muon` but I realise that the combination of older versions of `muon` and newer versions of...

@bioarpit1 This has to be implemented on the AnnData's side: https://github.com/scverse/anndata/issues/796. Here, the solution is simply converting `OrderedDict` to `dict` where this issue arises.

We'll have it on confa-forge, I think scanpy is also leaning towards just using [conda-forge](https://anaconda.org/conda-forge/scanpy). There's been one mildly annoying thing that we can't get `.tar.gz` source files from PyPI...