Best current tool for deconvolution of bulk sample
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6 months ago
changxu.fan ▴ 50

Just asking around for some general opinions: I will receive bulk RNA-seq and ATAC-seq samples from the spleen (they are all immune cells). To have an idea about the percentages of each individual cell type in the bulk sample, what would be the tool you guys recommend? Immune cells are pretty well defined. I'm almost certain that I can find single cell data or highly purified bulk data for all possible populations.

Thanks~

cibersort • 350 views
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Hello, it depends of your samples. If your looking to describe the immune cells, MCPcounter and Cibersortx with LM22 signature are near perfect for you. The both tools works pretty well. MCPcounter has more general cell types (10 cell types, no subtypes) and is more adequate to describe the Tumor Micro Environment while Cibersortx will describe over 22 immune cell types. So, you won't need to create your own reference at start. You can use Cibersortx on their website : https://cibersortx.stanford.edu/ and MCPcounter on R, it's a package very easy to use.

Hope it helps you !

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