• R (packages: edgeR)
• Python (packages: pandas)

Rscript step0_preprocess.R

Rscript step1_calculateStats.R 

Rscript step2_findRef.R

Since the example dataset has 115 samples in group1.

Rscript step3_overlapFisher.R 115

Rscript DDR_Ref.R

If you have another python version that has pandas:

Rscript DDR_Ref.R PYTHON_PATH

• final_out.csv: Normalized count data
• ref_cpm_BRCA.csv: Expression of reference genes
• overlap_test_fdr_1_BRCA_DEC.csv: Differentially expressed genes with fdr < 0.1
• overlap_test_fdr_05_BRCA.csv: Differentially expressed genes with fdr < 0.05