Daniel Dimitrov

Hi @gomez-dan, 1. Are you saying that your data doesn't have any of those, but liana finds some? It's quite a simple row/colSums that checks if there are any genes/cells...

Hi @divyanshusrivastava, Currently, there is no plan to add caligraphy. Although, this might change when liana changes its main developer :) We also welcome contributions, in case this was the...

Hi @Rafael-Silva-Oliveira, Now, the bandwidth is I assume is being calculated in pixels, i.e. the x,y units stored in adata.obsm['spatial']? And pixels in Visium HD images should correspond to something...

Hi @Rafael-Silva-Oliveira, You could try setting add categories and mask negatives to false. Perhaps, this is causing the issue. If it is, I could have another look as there might...

Hi @huiyijiangling, I'm pretty sure it's just a versioning issue. Please update liana: `pip install liana --upgrade`

Hi @Zach-Sten, you're right this is currently not possible. But I see your point how it can be useful. Are you more interested in the multi-view or the single-view models?...

Hi @Zach-Sten, thanks for the info. If you are interested in multi-views then Misty fits well. If you want to see specific tissue cores (regions), perhaps the recent extension of...

Hi @jun-miao113, 1. By default, LIANA will filter out any cell type with less than 10 cells. Whether this is reliable would depend on how much you believe that a...

Hi @jun-miao113 1. You can adjust it, there is a parameter called min_cells. Also, you could filter your object manually - it's essentially the same. Not sure if cell number...

Hi @demian1, I agree with the idea that maybe doing filtering independently makes sense. Perhaps, besides the obvious of setting everything to (e.g. 0 or infinity depending on the filter),...