In satijalab/seurat: Tools for Single Cell Genomics

To install Seurat, R version 4.0 or greater is required. We also recommend installing R Studio.

{#id .class width=60 height=60} Seurat 5: Install from GitHub

Copy the code below to install Seurat v5:

remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)

The following packages are not required but are used in many Seurat v5 vignettes:

SeuratData: automatically load datasets pre-packaged as Seurat objects
Azimuth: local annotation of scRNA-seq and scATAC-seq queries across multiple organs and tissues
SeuratWrappers: enables use of additional integration and differential expression methods
Signac: analysis of single-cell chromatin data

remotes::install_github("satijalab/seurat-data", "seurat5", quiet = TRUE)
remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)
remotes::install_github("satijalab/seurat-wrappers", "seurat5", quiet = TRUE)
remotes::install_github("stuart-lab/signac", "seurat5", quiet = TRUE)

Seurat v5 utilizes BPCells to support analysis of extremely large datasets:

remotes::install_github("bnprks/BPCells", quiet = TRUE)

For more information on BPCells installation, please see the installation instructions. For macOS users, the following GitHub issues concerning M1 chip installation and compiler compatibility may be of use.

Install from CRAN

Seurat is available on CRAN for all platforms. To install, run:

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

If you see the warning message below, enter y:

package which is only available in source form, and may need compilation of C/C++/Fortran: 'Seurat'
Do you want to attempt to install these from sources?
y/n:

Install previous versions of Seurat

Install any version 3 release

Any of the Seurat version 3 releases can be installed with the following command:

remotes::install_version("Seurat", version = "3.X.X")

Install the last version 2 release (2.3.4)

To facilitate easy re-installation of the last version 2 release, we are hosting the binaries on our website. These can be installed with the following command:

source("https://z.umn.edu/archived-seurat")

View the script

Older versions of Seurat

Old versions of Seurat, from Seurat v2.0.1 and up, are hosted in CRAN's archive. To install an old version of Seurat, run:

# Enter commands in R (or R studio, if installed)
# Install the remotes package 
install.packages('remotes')
# Replace '2.3.0' with your desired version
remotes::install_version(package = 'Seurat', version = package_version('2.3.0'))
library(Seurat)

For versions of Seurat older than those not hosted on CRAN (versions 1.3.0 and 1.4.0), please download the packaged source code from our releases page and install from the tarball.

Install the development version of Seurat

Install the development version of Seurat - directly from GitHub.

# Enter commands in R (or R studio, if installed)
# Install the remotes package
install.packages('remotes')
remotes::install_github(repo = 'satijalab/seurat', ref = 'develop')
library(Seurat)