Comments (4)
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.
Related Issues (20)
- Modernize CI HOT 4
- Support for mouse deconvolution HOT 3
- patched mcp counter dependencies
- quantiseqr / immundeconv differences HOT 2
- quanTIseq update HOT 2
- Error in Installation of R Package HOT 2
- Error in the mapping of cell types HOT 1
- TPM-normalized HOT 1
- genes not being identical between reference and my gene expression data HOT 15
- GLIBCXX_3.4.30 not found when trying to use timer HOT 1
- Issue with ESTIMATE inner_join() HOT 3
- Wrong names of ESTIMATE scores HOT 7
- deconvolute_consensus_tme won't work with "Unfiltered" indications HOT 1
- Error message when running CIBERSORT HOT 16
- Error in deconvolute_cibersort HOT 7
- Hi what is the original article to BASE method for deconvolute_mouse()? HOT 1
- Immunedeconv terminates for (non-)duplicate gene symbols HOT 7
- Error by using mouse_genes_to_human function HOT 1
- Unable to load immunedeconv HOT 12
- Error running cibersort HOT 3
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