This repository is for single cell RNA sequencing analysis related to Lawlor, Vanslambrouck, Higgins, et al, Nature Materials, 2020. Imaging analysis is in the repository KidneyRegeneration/BioprintedOrganoids-imaging.
All data needed to replicate the single cell RNA seq analysis is at :
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152014
Each of the conditions, Ratio0 ('dots'), Ratio40 ('line'), Man ('hand') has an associated set of CellRanger output matrices containing the mRNA data as well as a set of CITE-seq-Count output matrices containing the hashing data.
The folder R-analysis contains the R notebooks that document the Seurat based analysis, including QC, clustering and differential expression testing.
R-analysis/Seurat-analysis-QC.Rmd describes the initial QC and incorporation of hash tag data.
R-analysis/Seurat-analysis.Rmd describes all other analysis.
Scrublet/run_scrublet.py is the script used to perform computational doublet prediction using scrublet.