This repository contains scripts for data processing, analysis and figure generation using scRNA-Seq and bulk RNAseq data for our paper:

Jerber*, Seaton*, Cuomo* et al., Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation, Nature Genetics, 2021.

The following folders contain scripts for data processing and analysis. A short description can be found below:

• Plotting Notebooks contains all jupyter notebooks to reproduce the individual figures (main and supplements).

• 10x Analysis Pipeline contains a snakemake pipeline to process the individual scRNA-seq files generated by the 10x CellRanger software.

• Neuronal differentiation outcome predictor contains a jupyter notebook and example data to predict differentiation outcome of iPSC lines based on iPSC gene expression.