Daniel Dimitrov

Hi @Flu09, I assume this error happens because you have set `build_only` to FALSE, and inplace is by default set to TRUE (yet you have no sce object). I can...

Hi @Flu09, > I am not sure why there is only one tensor dimension, not sure if I understand how your tensor is 1 dimension, as your tensor$shape print shows...

Hi, This is likely related to perhaps using CellChatv2? I tried the latest version from the now archived CellChatv1 with which liana was designed to work with and it worked...

Hi @Mona1982, I believe a single GPU w 48GB memory should be sufficient given that the step with tensor-cell2cell is done after the data are aggregated by sample. So, the...

Here you can find extensive tutorials: https://ccc-protocols.readthedocs.io/en/latest/ And instructions how to set up a gpu env: https://github.com/saezlab/ccc_protocols/tree/main/env_setup

Hmm this is a bit odd. Can you check that cuda is available in your env, and also that you request enough video memory via the nvidia-smi log. EDIT: https://enterprise-support.nvidia.com/s/article/Useful-nvidia-smi-Queries-2...

Hi @Mona1982, Great. Apologies for the basic suggestions, users with different backgrounds use liana so I have to double check. I'm currently on patternity leave and won't get a chance...

Hi @Mona1982, If you are interested in metabolite-mediated CCC, you could follow this tutorial: https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#Metabolite-mediated-CCC-from-Transcriptomics-Data You could also pass Neuronchat as the sole resource to liana, though there might be...

1 & 3 are fair points :); 2 is largely covered, but I agree maybe coverage can be increased a bit there

Hi @min0609, Unfortunately, I have not encountered this error, so I cannot say anything beyond the fact that the loss seems to be None - likely suggesting that something is...