Preprocessing-and-analysis-of-FANTOM5-CAGE-profiles

(1) CAGEr package was used to preprocess the CAGE peaks including mapping, annotation, and resulting in the gene expression matrix which was used for the analysis.
(2) DESeq2 package was used to perform differential expression analysis for each of ADMSCs, NSCs, and Neuorns vs. the background samples. Details of profiled samples are included in Table S1.