Code and data for : Stem-cell states converge in multi-stage cutaneous squamous cell carcinoma development

This repository includes code and processed data required to reproduce all analyses and figures from The study by Taylor & Kandyba et al "Stem-cell states converge in multi-stage cutaneous squamous cell carcinoma development."  This repository includes:

1. pp2ai_taxol_analysis_Rscript.R  provides R code to process and analyze bulk expression data from 2 mouse tumor cell lines treated with a PP2A inhibitor and paclitaxel.
2. integrated_corrected_cds_v3.RDS is an R object in the cell dataset format for single-cell RNA sequencing expression of the original experimental samples.
3. pp2ai_taxol_mapping_script.sh provides bash script to map bulk expression reads.
4. Aim2-4.zip provides bulk expression data for normal skin and carcinoma samples used to generate Spearman rank correlation networks and metagenes.
5. Combined data set from Genome Biol 2011.zip provides bulk expression data for independent normal skin, papillom, and carcinoma samples used to generate Spearman rank correlation networks and metagenes.
6. scRNAseq_analysis_code.R provides R code to generate all analyses and figures found in the study.
7. chemotherapy_additional_samples.RDS is an R object in the cell dataset format for single-cell RNA sequencing expression information from the cisplatin experiment (4 control carcinomas + 4 cisplatin-treated carcinomas) and independent papillomas (7 additional papillomas).