Daniel Dimitrov

Hi @dertrotl, Thanks a lot for raising this issue. I encountered it also myself, it seems like AnnData now enforces specific types in obsm, and one can no longer assign...

PS. tbh, I couldn't think of an elegant way to fix this such that one can save in place. Commonly, people would store a matrix in obsm, and then auxiliary...

Hi @tuhulab, Please make sure to update liana+ to the latest version. This should resolve the issue: `pip install liana --upgrade`

Hi @whitneyt1, You could indeed aggregate the results by passing e.g. mean as a function to `aggregate_fun` of the visualizations for misty. You would need to pass a concatenated dataframe...

Hi @whitneyt1, Yes, exactly. You could also see matplotlib versions of these plots with a condition here: https://github.com/saezlab/lianaplus_manuscript/blob/main/notebooks/sma/sma_plot.ipynb Hope this helps.

Hi @shanggutianzhen, I will make sure to remove the restriction in the next update. Daniel

Hi @csennis, Thanks for using liana and apologies for the delayed response. Hmmm, if I remember correctly about SCT transform as long as you use the counts rather than the...

Perhaps, it's best if you follow the notebook I referred you to in the other issue. It seems here that there might be some issue with the liana results stored...

Hi @mainharryHR, LIANA when combined with Tensor-cell2cell supports any number of conditions. I would refer you to this tutorial where we look at 3 conditions at the same time: https://ccc-protocols.readthedocs.io/en/latest/notebooks/ccc_R/QuickStart.html,...

Hi @mainharryHR, See the factors and hence factor loadings that you get are summaries of the signal across all your samples. So, the plots do work across an indefinite number...