Any tools to estimate the relative abundance of immune cell in tumor
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3.1 years ago
CY ▴ 610

I am on a project that need to estimate relative abundance of immune cell in tumor. Anyone know any tools can do that? Thanks a lot for any comments.

RNA-Seq immune fraction absolute estimate • 1.1k views
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Based on your tags this looks like an RNA-seq question. But it would have been nice if you could explain your question a little better. Anyway, the term you are looking for is called "deconvolution".

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Sorry. My project is to estimate immune composition in tumor sample. Tools like SIBERSORT only gives relative abundance of each immune composition. I was trying to estimate an absolute abundance by adjusting the relative abundance by immune fraction. Then I realized this is kind of useless because such absolute abundance of immune composition is also biased by the extracted tumor sample itself, right?

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3.0 years ago

Take a look at ESTIMATE

(Estimation of STromal and Immune cells in MAlignant Tumours using Expression data)

Kevin

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