library("DESeq2")
library("tximport")   
#Differential expression analysis of mrna
setwd("C:/Users/Administrator/Desktop/STRESS/MRNA")
dir="C:/Users/Administrator/Desktop/STRESS/MRNA"
list.files(dir)
sample <- paste0(seq(1,6),".tsv")
files <- file.path(dir,sample)
names(files) <- paste0("sample",c(1:6))
txi <- tximport(files, type = "kallisto", tx2gene = tx2gene_cDNA_homo)
sampleTable <- data.frame(condition = factor(c("C","C","C","S","S","S")))
rownames(sampleTable) <- colnames(txi$count)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition)
dds <- DESeq(dds,parallel = T)
vst <- vst(dds)
plotPCA(vst)
res <- results(dds) 
write.csv(res,"DEmrna.csv")

#Differential expression analysis of microRNA
setwd("C:/Users/Administrator/Desktop/STRESS/microRNA")
mirna_count <- read.csv("C:/Users/Administrator/Desktop/STRESS/microRNA/mirna_count.csv", row.names=1)
condition <-factor(c("C","C","C","S","S","S")))
coldata <- data.frame(row.names = colnames(mirna_count), condition)
dds <- DESeqDataSetFromMatrix(countData=mirna_count, colData=coldata, design=~condition)
dds <- DESeq(dds,parallel = T)
vst <- vst(dds)
plotPCA(vst)
res <- results(dds)
write.csv(res,"DEmicroRNA.csv")