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Installation Instructions for Seurat

If you have installed a previous version of Seurat, it is recommended that you restart your R session before loading the new version. First install R and the devtools package. NOTE: there have been some compatibility issues with R 3.4.0. We recommend reverting to R 3.3.3 until these are resolved. For those on running Ubuntu, see this post for a potential solution.

  1. Install R (v >= 3.2)
  2. Recommended : Install R Studio
  3. Install the “devtools” package from Hadley Wickham

    # Enter commands in R (or R studio, if installed)
    install.packages("devtools")
    library(devtools)
    

Instructions for Mac

Install From Release Binaries

Install Seurat - directly from Github.

install_url("https://github.com/satijalab/seurat/releases/download/v1.4.0/Seurat_1.4.0.16.tgz", binary = TRUE)
library(Seurat)

You will need to be running a recent version of R (R >= 3.3.3) for this to work properly. You can find that here. If you want to use a different version of R, you may need to install from source.

Install From Source

Install Seurat - directly from Github.

install_github("satijalab/seurat")
library(Seurat)

This may cause errors on some standard Mac installs due to R being compiled using gfortran-4.8. They will look something like

-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran

To fix this, refer to the following blog post. NOTE: you will need sudo permissions.

Another potential solution to this issue that doesn’t require sudo permission (credit to Michael Steinbaugh) can be found here.

Installation on Windows

  1. Install R (v >= 3.2)
  2. Recommended : Install R Studio
  3. Install the “devtools” package from Hadley Wickham

    # Enter commands in R (or R studio, if installed)
    install.packages("devtools")
    library(devtools)
    
  4. Install Rtools

  5. Ensure that Java is installed.
    • Open CommandPrompt and type java -version
    • If this doesn’t return a version of java >= 1.6, download the latest Java SDK from Oracle and run the installer.
    • Restart the R session
  6. Install Seurat - directly from Github.

    install_github("satijalab/seurat")
    library(Seurat)