Gregor Sturm

> The only thing that bothers me is a future warning raised while using logomaker.alignment_to_matrix() as I am not sure if this will become a serious issue in the (near)...

I've seen one example in a paper where they * put logoplots of VJ / VDJ seqs next to each other * also made logos of VDJ gene usage. See...

Thanks @MKanetscheider, I think I can take it from here! I'll apply some final cosmetic touches and then merge it :)

it's tracked on the differentialabundance side, not sure we need the ticket here: https://github.com/nf-core/differentialabundance/issues/367

thanks for reporting... gtfparse again, I should try to get rid of that package somehow.

I believe the best solution is to introduce alternative ways of retrieving the genomic positions, see https://github.com/icbi-lab/infercnvpy/issues/144

You have a very old version of `pyarrow` installed. I don't know how you end up with that version in a fresh environment, but can you try updating it? (latest...

Have you tried subsetting your `adata` before plotting, something like ```python adata_sub = adata[:, adata.var["chromosome"].isin(["chr1", "chr7"])] cnv.pl.chromosome_heatmap(adata_sub, ...) ```

Sorry, my bad. `infercnvpy()` writes the result to `.obsm` since it does not have exactly the same number of features (since several genes are merged into bins, and some genes...

What do you mean by "scale"? length in base pairs?