This is the analysis code of the scRNAseq data from paper: The Cellular Diversity and Transcription Factor Code of Drosophila Enteroendocrine Cells.

Region specific gene enrichment (RSGE) arthrogram To evaluate the regional preference of each cluster, we used the bulk EE RNA-seq data of different midgut regions from the Flygut-seq database (http://flygutseq.buchonlab.com/resources) (Dutta et al., 2015). For each region, genes with RPKM >= 3.5 and fold enrichment over other four regions more than 2.5 were profiled, and the top 100 genes according to fold enrichment were selected as the region-specific gene sets to perform subsequent analysis. To evaluate whether cells from scRNA-seq data express certain genes, we set a cutoff with the scaled value of 0.5, and then calculated the percentages of the cells expressing these region-specific genes in each cluster. The summed percentages of the 100 genes of each region were represented as the regional enrichment score for each cluster.

To investigate peptide hormones co-expression patterns at single cell level, we set the scaled value 0.5 as the threshold to distinguish whether a peptide is expressed or not. Totally 14 peptide hormones were composed in this step. The barplot of peptides combination was made by R package ggplot2.

TF code analysis, please see felixhorns/FlyPN

We also provide an online scRNAseq data query portal.