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I would like to find the proportion of each cell-type in bulk RNA-Seq transcriptomics data. I am looking for some guidance on the following:

  • What are the state-of-the-art methods?
  • What are their assumptions? (e.g. do they assume that cell-type expression signatures are available in advance?)
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  • $\begingroup$ Can you describe your experimental design further? This is often solved with single cell RNA-seq $\endgroup$ Jun 23 '20 at 11:50
  • $\begingroup$ It's not my experiment - I am just trying to deconvolve bulk RNA-Seq data from a publicly available database (GTEx), e.g. given a whole blood sample, find out the proportions of each cell type (e.g. lymphocytes, macrophages,...). Any suggestion? $\endgroup$
    – rvinas
    Jun 24 '20 at 7:43
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I see a lot of people using xCell. There should also be papers systematically compare many different methods, which might interest you.

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  • $\begingroup$ Thanks for the pointer. Do you have any reference of a good up-to-date review paper? A simple description of the methods and requirements would be highly appreciated too $\endgroup$
    – rvinas
    Jun 24 '20 at 7:45
  • $\begingroup$ This one looks promising although it may not cover all the methods biorxiv.org/content/10.1101/2020.01.10.897116v1.full.pdf $\endgroup$
    – Phoenix Mu
    Jun 24 '20 at 15:23

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