Tumor_Microenviornment

1.Differential expression analysis

1.1 Scirpt

DEA.R

1.2 input

① IDs of control gorup (.txt file)
② IDs of treat group (.txt file)
③ TCGA project name (the script would download both clinical and expression matrix automatically with the project name)

example:
Rscript DEA.R ./test/control.txt ./test/treat.txt TCGA-ESCA

1.3 output

output files listed below:

result

DEA

DEG.txt: differential expression analysis result file
heatmap.png: heatmap for DEGs
volcano.png: volcano for DEGs

result

Stemness

stemness.txt: stemness score of each patients

2.TME

2.1 Scirpt

Immune.R

2.2 Input

① RNA-Seq file path ② IDs of control gorup (.txt file)
③ IDs of treat group (.txt file)
④ parameter：mean OR median to define score cutoff
⑤ survival parameter: OS/DFI/DSS/PFI
⑥ gene names that you focus

example:
Rscript.exe Immune.R ./result/RNAExp.txt ./test/control.txt ./test/treat.txt mean OS SOX2,TP63

2.3 Output

result

Immune

estimate_score.txt:Stromal and Immune Score of each patient
estimate-ttest.png:violin plot of Stromal and Immune score of two groups (input groups) with p-value(student's t test) estimate-survival.png: two groups (divided by mean/median) survival analysis with p-value
xCell_ttest.txt: student's t test result of each cell compounds between input groups. Four columns including cell name, mean of control group, mean of treat group and p-value

result

xCell-ttest: visualizaiton of t-test result which p-value less than 0.05
Gene name (example:SOX2): 64 pngs of correlation plots between gene expression and cell compounds.