Project Title: PD-L1 activity is associated with partial EMT and metabolic reprogramming in carcinomas
Description: The codes in this repository can be used for a) generating gene expression matrices by processing microarray or RNA-seq transcriptomic data from public repositories online such as NCBI GEO and EMBL ENA
b) quantifying EMT activity using various scoring methods such as single sample gene set enrichment analysis (SSGSEA), 76GS (as described in Byers et. al., 2013) and KS (as described in Tan et al., 2014)
c) quantifying metabolic activity of glycolysis, OXPHOS, and fatty acid oxidation (FAO) using SSGSEA.
d) quantifying expression levels of immune genes and signatures from the gene expression matrices.
e) calculate survival analysis of TCGA cancer cohort within the context of EMT and metabolism ( glycolysis, OXPHOS and FAO)
Install all necessary R and Python packages for running the codes successfully.