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omnideconv / immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods
https://omnideconv.org/immunedeconv/index.html
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Return missing genes for each tool #95

Open anabbi opened 2 years ago

anabbi commented 2 years ago

Hello,

Depending on many factors, number of genes matching between input gene matrix and reference genesets can vary and depending on the tool, it can sometimes add variation in the output. It would be great if deconvolute can return a warning of missing reference genes so the user be cognizant of any downstream discrepancy.

In the long run, it would be great to "harmonize" all tools with stable IDs such as Ensembl IDs.

Thanks for your great package!

grst commented 2 years ago

Hi @anabbi,

that's certainly a good idea! I think some methods already raise such a warning, but I agree that it would be nice if there was a consistent message for all tools.

Regarding the gene identifier: All of the tools use HGNC gene symbols in their signatures. I'm not so sure it would be worth re-mapping those to ensemble IDs as they would anyway just be based on the gene symbols.