Question: Deconvolution RNA-Seq data
0
gravatar for carleshf
4.7 years ago by
carleshf10
Spain/Barcelona/ISGlobal
carleshf10 wrote:

Dear all,

I am working with human blood samples in a DE genes analysis. Now we want to perform the deconvolution of the matrix of counts to see the different cell types. My idea is to follow the guidelines described herehere and here but with RNA-seq data. I found that the R package DeconRNASeq can do it, as explained here. But, as far as I understand, the matrix-signature for each type of cell is required.

My question is: Where can I get the signatures for usual cell types present in blood to be used with DeconRNASeq?

Tanks,

C.

ADD COMMENTlink modified 4.7 years ago by James W. MacDonald51k • written 4.7 years ago by carleshf10

Dear C.

 

Did you find a specific signature to use with DeconRNASeq?

Best

Daniel

 

 

ADD REPLYlink written 4.2 years ago by dtiezzi0
Answer: Deconvolution RNA-Seq data
1
gravatar for James W. MacDonald
4.7 years ago by
United States
James W. MacDonald51k wrote:

The 'signatures' are simply RNA-Seq counts on purified samples of each cell type. You would get those the usual places; either do the work in your lab, or try to find some publicly available data (the SRA would be the logical place to look).

ADD COMMENTlink written 4.7 years ago by James W. MacDonald51k
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