Any tools to estimate the relative abundance of immune cell in tumor

Question

[CY]

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.

[WouterDeCoster]

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".

[CY]

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?

Answer 1

[Kevin Blighe]

Take a look at ESTIMATE

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

Kevin