Clubcell_Organoid

This repo contains the R code for the JPath scRNA-seq analysis

This code takes in the denoised (decontX) .rds scRNA-seq object as input and could achieve the following:

1. Separate cells by treatment condition
2. Separate cells by AR status
3. Compute signature scores from previously established signature gene sets
4. Use pheatmap to make heatmaps of canonical markers or customized gene sets
5. Compare signature scores of two AR response signaling pathways between cells of different AR status or treatment types

The .rds object and signature gene sets could be found here: https://www.dropbox.com/sh/pp5gkhqd7lokb1k/AAAf4VZ9RKjr6bPopfT3a7Sra?dl=0