Scripts and resources for the manuscript titled as Recent evolution of the developing human intestine impacts metabolic and barrier functions (Yu, Kilik, Secchia et al)
DEG_and_DAR: scripts to identified differentially expressed genes (DEGs) and differentially accessible regions (DARs) between human, chimpanzee and mouse.
Data_preprocessing_integration_and_annotation: scripts to construct customized reference for read alignments where applicable, preprocessing, integration and cell type annotation for scRNA-seq and scATAC-seq data.
Deep_learning: scripts to perform sequence variation modeling based on ChromBPNet and the derived models.
Evolutionary_force: scripts and resources for deepest evolutionary ancestry assignment for regulatory elements and calculation of dN/dS.
Plotting: plotting scripts, including script to generate willow plot for visualization of hierarchy of enriched GO terms and parent terms and coverage plots with overlapping genomic signature.
scSTARRseq: scripts to construct customized reference for read alignments, preprocessing and downstream analysis.
In this manuscript, Stefano Secchia established the workflow for scSTARRseq data analysis, Christiana Fauci established the workflow for deepest evolutionary ancestry assignment; Jasper Janssens established the workflow of deep learning. Qianhui Yu established the other workflows and are responsible for the maintenance.