Chananchida Sang-aram
Chananchida Sang-aram
I've implemented a fix for the wrapper functions now. Please update to v2.0.6 and let me know if there would be any issues. Note that the alias conversion function will...
@avpatel18 Is it the same error as above? Could you also provide your `sessionInfo()`?
You cannot set the gene set of interest as the same as the background. NicheNet looks for the enrichment of the gene set of interest within the background, so setting...
Hi, This indeed could be an issue with your Seurat object - can you run `Idents(seurat_obj)` to see what comes out? If there's no identity that was set, you can...
Hi all, I will be working on fixing this ASAP, although it may take a while because I want to ensure that everything is still compatible with the previous Seurat...
Hi all, This issue has been fixed in NicheNet v2.0.4. The vignettes and functions should now work with both Seurat v4 and v5. As @jessicaliu70 mentioned, the issue was indeed...
Hi, indeed as you have said, it's not possible to define two receiver cell types in the Differential NicheNet pipeline. This is also mentioned in the vignette. It's also partly...
Hi @shawnshu1, Thank you for noticing the bugs and providing a solution. Apologies for taking some time to get around to this. In the pull request, I have incorporated your...
No, we did not consider the protein complexes. This is because we did not want to be too stringent with the filtering, i.e., requiring all subunits of the complex to...
Hi, You're indeed correct! The issue is with this line: ``` vis_ligand_lfc