This folder contains scripts used for analysis of single-cell RNA-seq data in our recent definitive endoderm screen. (For atacTFAP analysis, there is a separate repo.)
You can find the data at GEO: GSE127202. You will need a couple of key R packages: Seurat version 2 (from the Satija lab) and thymusatlastools2 available here. We also use freezr to save code and session info and to track processed data for use in downstream scripts. To install the correct versions, try the installation script provided in scripts/install.R.
main.R is the master script for the paper draft. To reproduce the paper,
- in
main.R, edit the variableproj_dirto point to this repo, - in
clustering/setup.Rmd, edit the lines that read in the data. - in
clustering/integrate_gAmp.Rmd, edit the lines that read in the data.
Then run main.R line by line.
We're passionate about reproducibility, but we understand that exact reproduction across environments is very difficult. If you have trouble, please file an issue on github.