Daniel Dimitrov

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Hi @jjacob12, I was able to, thanks for sharing. I'm mid revisions of 2 papers but I will come back to you as soon as I find some time. Sorry...

OmniPath's PPI network can be used to find downstream TFs in a sign-coherent way, see fig 4 here: https://www.biorxiv.org/content/10.1101/2023.08.19.553863v1

Hi @BenjaminDEMAILLE, Thanks for pointing this out! I will replace it in the next liana update, together with the other open issues :) Daniel

Hi @achilessss, Can you please post a reproducible example or your `rlang::last_error_trace` + R session info? I could then check if there is something different, etc.

Hi @sakinaamin, Sorry for the delayed response, I must've missed it. I can't see anything in the session that might be out of the ordinary, perhaps if you could provide...

Hi @shenscore, Likely the easiest way would be via the OpenProblems repo, where we reproduced and extended the benchmark described in the liana manuscript: https://github.com/openproblems-bio/openproblems/tree/main/openproblems/tasks/_cell_cell_communication Hope this helps :)

Hey, Thanks for the issue. Though I am unable to reproduce it. This seems to be somehow related to Windows? I found an issue where it was resolved by cloning...

Thanks Rene @welch16 I will make sure to change this in the next update :)

PS. Please note that I bumped the version down to 4.1, simply not many people use 4.2 yet (I know BioC requires this) and if I'm to have an update...

Hi @lindsdudley, Can you please share which tutorial is this from? Input data is usually a SingleCellExperiment or Seurat object. Does this help?