Gregor Sturm

Closed via #562

I now have a use-case where this becomes an issue: I would like to add a column to `obs` that contains an object holding T-cell receptor chains for each cell....

I am experimenting with storing T cell receptor data from, e.g. 10x VDJ sequencing in the AnnData object. Ultimately, I want to build a scanpy extension for single cell TCR...

@ivirshup, it indeed does not work... I mistyped a variable name when testing :/ @davidsebfischer, I would be curious to learn about your project and potentially avoid duplicated efforts ;)

Initially, I had hoped to stick with standard `AnnData`, s.t. `h5ad` files stay compatible with systems on which the tcr-library is not installed. But it might the way to go!...

Hi @davidsebfischer, thanks for joining in! > Hi all, there is an bunch of extra type of preprocessing methods associated with the TCR / BCR data. Would you mind providing...

Would be better to fix this, rather than just raising a warning. Possibly by escaping/unescaping `/` in dict keys on save and load, but maybe there's a better solution.

Hi @falexwolf, thanks for explaining all that! I wasn't aware of the way the `highly_variable_genes` works, I had still been using the deprecated `filter_genes_dispersion`. I agree that simply annotating the...

2.0.0 is a very old version and many things have been improved since then. Is there any reason why you use that version? The results should be in the `salmon`...

hmm, seems support for 10xv1 got removed from alevin at some point. It is still possible to specify the chemistry using a description such as `1{b[16]u[10]x:}2{r:}` (this is for 10xV2,...