Q:
I would like to apply the bulk-tissue deconvolution algorithm in your recent paper (Wang et al., 2018) using our own single cell RNA-Seq data and Gandal et al., 2018’s bulk tissue RNA-Seq. I couldn’t find code related to the deconvolution steps in the Gernsetin Lab github page (https://github.com/gersteinlab/PsychENCODE-DSPN) or on the PsychEncode resources page. I only found results to the cell fraction calculations. Would you be able to point me towards how I can apply this algorithm?

A:
We used non-negative least square method for deconvolution and implemented it using R function nnls (https://www.rdocumentation.org/packages/lsei/versions/1.2-0/topics/nnls) For example nnls(C, bi) estimates the cell fractions for ith tissue sample, where C is cell type gene expression matrix (row: gene, column: cell type), and bi is the gene expression vector for ith tissue sample.