Is it possible to extract cell-type specific expression from my datamatrix? about immunedeconv HOT 4 CLOSED

Hi klai001,

thanks for your question.
If I got you right, what you want to do is "complete" deconvolution.
The methods in immunedeconv only support "partial" deconvolution -- so no, this is not possible.

You might want to have a look at the new CIBERSORTx method for that.

Cheers,
Gregor

from immunedeconv.

Hi Gregor
thank you for the tips!
Would we then be able to retrieve the gene signatures for each method we run through immunedeconv into a vector?

from immunedeconv.

With "gene signatures", are you referring to the signature matrices?

The quantiseq and EPIC signatures are here and here, respectively. The CIBERSORT matrix is only available upon registration from their website.

The other methods use different approaches altogether... See our paper for more details.

from immunedeconv.

Yep, Thanks for the materials Gregor!

from immunedeconv.