The pecora (permutation conditional random) package provides functions to perform the one-sample and two-samples t-tests using permutations/sign-flipping.
To install it:
devtools::install_github("angeella/pecora")
library(pecora)A toy example:
X <- matrix(rnorm(10*100000,5,sd=5),100000,10)
system.time(out1 <- oneSample(X,1000))