DESeq

 # Loading the library
 library("DESeq2")
 # Reading and preparing data
 c<-read.table("m.txt",head=TRUE,row.names = 1)
 c<-round(c)
 colData <-read.table("colData.txt",head=TRUE,row.names=1)

 # Running DESEQ
 dds<-DESeqDataSetFromMatrix(countData=c,colData=colData,design= ~ condition)
 dds <-DESeq(dds)
 res  <- results(dds)
 resOrdered <-res[order(res$pvalue),]
 write.csv(as.data.frame(resOrdered),file="set0.csv")
 
 # MA plot
 plotMA(res,main="MF",ylim=c(-5,5))

 # Printing differentially expressed genes
 head(resOrdered)
 resSig <- subset(resOrdered,padj<0.1)