EMT score calculation

This code downloads microarray GEO data for a given GSE ID, preprocesses it to generate gene wise expression and calculates EMT score using methods mentioned in Byers et al.,2013, Tan et al., 2014 and George et al., 2017

To run the code successfully you should have all the required R packages installed.

Please run the code in R as follows :

setwd(“./EMT_score_calculation”) (**note: depending upon where you save it in your desktop change the working directory)

system(paste(“Rscript ./EMT_GEO.R”, <"GSEID">))

If you find this code useful in your research, please cite

Chakraborty et al. Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum. Front. Bioeng. Biotechnol. 8:220. doi: 10.3389/fbioe.2020.00220