Question: Options for cell type deconvolution from whole blood?
gravatar for penny.lane
16 days ago by
penny.lane0 wrote:


My colleagues and I have human, whole blood RNA-Seq data from which we would like to estimate the proportions of various immune cell types within each sample and then see how they are changing between samples. We do not, however, have our own matched single cell RNA-Seq data set to help with the deconvolution. What methods would people recommend we consider? We're particularly interested in any methods that have already been validated to work well on whole blood samples.


rna-seq • 106 views
ADD COMMENTlink modified 14 days ago by trausch1.4k • written 16 days ago by penny.lane0
gravatar for trausch
14 days ago by
trausch1.4k wrote:

Cibersort could be an option.

ADD COMMENTlink written 14 days ago by trausch1.4k

Yeah, this is one that caught my attention, but according to their website the LM22 signature was designed & validated on microarray data and they warn against applying it to RNA-Seq data. They say they are in the process of deriving and validating a signature for RNA-Seq data, but no release dates are given. Any other ideas?

ADD REPLYlink written 13 days ago by penny.lane0
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