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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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Cellphonedb for proteomics analysis #193

Open harshagr21 opened 5 months ago

harshagr21 commented 5 months ago

is:issue is:open can we use cellphonedb for proteomic data analysis. i have relative abudance of proteins among different samples (cells from different tissues.

ktroule commented 5 months ago

Hi.

I'm not familiar with the particularities your data but my thoughts are: Technically you can use, as long as the input format is as the expected and your values are non-negative. Bear in mind that your values are relative, which will likely alter the interpretation of the results.

LisaSchweizer commented 6 days ago

Hi, I would post a follow-up question to the 'proteomic data analysis', thank you for your initial response. We have cell-type resolved proteomics data and I would like to run a CellPhoneDB analysis on these. The file that we would need to adapt is the 'h5ad' format as this is not compatible with the proteomics data output (e.g. csv with proteins as row names and each column is one sample). Is there a way that the tool would take such a (simple) proteomic input file? The 'h5ad' contains much more information and to me it is unclear which information content of this file CellPhoneDB actually used. Thank you!