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cbg-ethz / COMPASS

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Use Compass data with protein data #14

Open BenjaminPLille opened 8 months ago

BenjaminPLille commented 8 months ago

Hi, I use compass with mosaic from proteogenomic data. I would like to reuse the compass data (small sub-clones) with the phenotypic data to analyze the protein expression of the sub-clones. Is this possible? Many thanks for your help Benjamin

e-sollier commented 8 months ago

Hi,

COMPASS does not provide a direct analysis of subclone-specific expression data, but you should be able to do it indirectly. COMPASS outputs a _cellAssignments.tsv file (see https://github.com/cbg-ethz/COMPASS?tab=readme-ov-file#output), which indicates to which node in the tree each cell was assigned. I have never worked with Tapestri protein data so I don't know how it looks like, but I suppose you should be able to use the cell assignments to look at subclones-specific protein expression.