Gene expression analysis
REGRESSION
Raw data from the nCounter® platform was pre-processed through an iterative quality control and normalization framework (Bhattacharya et al. To identify differentially expressed genes (DEGs) before and after CaEP treatment, we used Wald significance test within the DESeq2 analysis framework (“DESeq” function from DESeq2 package (v.1.38.0)) (Love et al. We used the top (Linear support vector regression [31] was applied for cell type deconvolution of the gene expression data. The “safeTME” dataset (Danaher et al. 