I found a solution so I'll post it in case anyone needs some help in the future.
First I found the mean q95 for that period using the colquantile funtion
max79_84<-coredata(max_79_84)
max79_84<-max79_84[,2:5786]
xx79<-matrix(as.numeric(max79_84),ncol = 5785,nrow=2192)
q5_79<-colQuantiles(xx79,prob=0.05)
q79<-mean(q5_79)
Then I made a variable that will count the number of times that I have days above that temperature
n79<-0
tx95<-0
for (i in 1:6000) {
n79[i]<-0
tx95_79[i]<-0
}
After that I made a loop to check the temperatures in every case, count the variables
for (j in 1:6000) {
for(i in 1:2000){
if(xx79[i,j]>q79){
n79[j]<-n79[j]+1
}
}
}
for (i in 1:6000) {
tx5_79[i]<-(n79[i]/2000)*100
}