R scripts for scRNAseq analysis of midbrain organoids from human iPSCs
R notebook with filtering, integrating, clustering, annotating and looking at gene expression within clusters from two samples of three midbrain organoids. separate R scripts computational intensive processes used to explore clusters at different resolutions.
Analysis will be found in the manuscript: Mohamed, Nguyen-Vi, et al. "Midbrain organoids with an SNCA gene triplication model key features of synucleinopathy." bioRxiv (2021).
The raw data (FASTQ), CellRanger outputs and Seurat object with cell type labels are posted on GEO GSE186780.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186780