LucaTucciarone

head(meta) ``` celltype MM_555_AAACCCAAGTAGTCTC macrophage MM_555_AAACCCACAGGTATGG acinar MM_555_AAACCCAGTGATGTAA ductal MM_555_AAACCCAGTGGTTTGT acianr MM_555_AAACCCATCAGGAGAC ductal MM_555_AAACCCATCCGATAAC immune ``` unique(cellchat@idents) ``` macrophageacinarductalacianrimmunebetalymph_endoalphaactivated_stellateq_stellatemastREG+_acinardeltaendothelialschwannmuc5b_ductal Levels: REG+_acinar''acianr''acinar''activated_stellate''alpha''beta''delta''ductal''endothelial''immune''lymph_endo''macrophage''mast''muc5b_ductal''q_stellate''schwann' ``` cellchat@data ``` 6731 x 8823 sparse Matrix of...

Digging into the problem it comes out my data, that I repeat is coming from a pull of different samples and exp-points, has also been normalised in scanPy in this...

I tried doing that but I still cannot find it. I am kinda confused honestly

@sqjin If I do that it gives me back only significative interactions. I would need all interactions, also pvalue >0.05 to then perform fdr

Wow, we have the same questions and applications. Did you solve it?

Could u share what tools you landed on in the end? I tried their normalization but I get a ton of NaNs, I am running using SCT now, I shall...

Is there an idea of if/when this may happen? ATACseq its R limitations way more often than RNAseq, that's the whole point of bpcells in my opinion, so it would...

news on this?