Erick Armingol comments

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                                            Erick Armingol

Large number of significant interactions

Hi @joan-yanqiong! Yeah, I think that's something that happens due that cell2cell does not filter genes by the fraction of cells that are expressing them. LIANA does that, through the...

Large number of significant interactions

No, unfortunately I developed this before most recent tools came out, and I haven't had time to implement these filtering steps they include. I plan to add more stringent filtering...

Spatial LIANA x cell2cell analysis in R

Hi @Qirongmao97. If you are able to make a grid of your tissue you can assign the spots to each bin in the grid and annotate that assignment, for each...

liana_tensor_c2c error: All input columns must be contained in all dataframes included in 'context_dict'

Yes, the issue is related to the column names passed as input, one or more of them does not match the column names in the dataframes.

liana_tensor_c2c error: All input columns must be contained in all dataframes included in 'context_dict'

Hmm, everything seems right, maybe try passing columns explicitly: ``` sce

liana_tensor_c2c error: All input columns must be contained in all dataframes included in 'context_dict'

Not sure what this error could be about, exactly what code generated it? I suspect it could be due to negative values in your scores? Did you normalize/scale your expression...

Example not working

Hi @imerelli I don't recommend using that example. Instead follow any other on the readme: https://github.com/earmingol/cell2cell/blob/master/README.md. Regarding your issue, a quick way to solve is to add to your command...

The way to address TypeError: Passing a set as an indexer is not supported. Use a list instead.

Hi @Pangjing-Wu Thank you so much for the detailed report. I had tracked the issue before, but I forgot to implement the quick fix. This was caused because of newer...

Problems with the tensor pipeline at the Tensor Factorization step

Sorry I cannot reproduce your error just with the h5ad file. Could you export you tensor and upload that file instead? Here there is an example of how doing so:...

Problems with the tensor pipeline at the Tensor Factorization step

I see! You are using the tensor-cell2cell analysis without LIANA, right? If so, in the step of creating the interaction tensor you need to add ```upper_letter_comparison=False``` to keep the names...