Daniel Dimitrov

Hi @grimbough, Thank you so much for your prompt response! Indeed, it was an inappropriate symbol in the .Renviron.

PS. I optimized it a quite a bit since we last spoke and it takes ~15 seconds for 5,000 interactions /w complexes from LIANA.

Hi @akiss-me, Thanks for using liana. I'm not sure if it would be feasible due to the large number of interactions typically summarized by the chord diagram.

Hi @akiss-me, Yeah fair point, this would require some modifications to my current function, in the direction of showing magnitude instead of frequency. I do have a magnitude-focused chord diagram...

Thanks @akiss-me :)

Hi @AltayYuzeir, Thanks for your interest in LIANA. Thanks for the suggestion, I will certainly consider it in future updates to LIANA :) Daniel

Hi Enrique, Looks amazing! I will add SCpubr as a suggestion in LIANA's next update :) Regards, Daniel

One suggestion would be that for the LR doplot, instead of filtering to only 'top hits': https://github.com/enblacar/SCpubr/blob/4a6033aa9171c7b4ad4ca8ec60dbd97f19f6cd38/R/do_LigandReceptorPlot.R#L170 I would instead filter to obtain 'relevant'/top-ranked interactions, then I would inner join...

This issue is now covered by SCpubr and I refer to it in the tutorial.

Hi @yjgeno, Actually, I have re-implemented the italk method completely under the "logfc" method, and hence the slower Seurat-based italk implementation is deprecated. The logfc method's required statistics, as well...