The easiest way to install it is currently the following: 1) Install a recent version of R from https://www.r-project.org/ 2) Optional: For ease of use, install Rstudio from https://www.rstudio.com/ 3) Open R and install all dependencies. Please ensure that you have writing permissions to install packages. Execute the following lines one by one: install.packages("devtools") source("http://bioconductor.org/biocLite.R") biocLite("GenomicRanges") biocLite("GenomicAlignments") biocLite("Rsamtools") library(devtools) install_github("ataudt/aneufinder") # Or alternatively if the above line doesn't work: install_git("git://github.com/ataudt/aneufinder.git", branch = "master")