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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))

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.