Giovanni Palla
Giovanni Palla
> CellPhoneDB has been updated to v3, which incorporate spatial information. Does sq.gr.ligrec adopt this version ? sorry am also not familiar with it, in which way does it incorporate...
hi @wangjiawen2013 , I think the way they incorporate spatial information is by simply subsetting the ligrec output with cell types that are known to co-occurr in visium spots, it's...
Hi @frankligy , I think you could set them to 0, what's the cluster composition of your dataset (e.g. how many obs per clusters) ?
unfortunately #437 does not address this but gets very close. Will keep this open for next release.
this would require to explicitly tell user that a new neighbor_graph will be re-run (but will not modify the anndata). I think it's a sensible solution but would change the...
Hi @aeisenbarth , thanks a lot for the interest and the suggestion. Indeed this is very important and beneficial for downstream use cases. We had something in mind very similar...
hi @simonmfr thank you for the interest in squidpy. For this type of question of best practices, I'd like to point you to https://discourse.scverse.org/ , you can ask the question...
hi @simonmfr , will close this issue due to inactivity, feel free to reopen if the problem persist.
thanks for interest in Squidpy @Tonyspuri , can you elaborate more what are you trying to do? I don't think is in scope to run lig_rec across different slides, so...
hi @JiaShun-Xiao thanks for the cotnribution, can you elaborate a bit more and provide code snippets about this PR? I don't think I fully understand teh settigns in which this...