Analysis, visualization, and integration of Visium HD spatial datasets with Seurat • Seurat

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

Seurat 5: 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)

Seurat does not require, but makes use of, packages developed by other labs that can substantially enhance speed and performance. These include presto (Korunsky/Raychaudhari labs), BPCells (Greenleaf Lab), and glmGamPoi (Huber Lab). We recommend users install these along with Seurat:

setRepositories(ind = 1:3, addURLs = c('https://satijalab.r-universe.dev', 'https://bnprks.r-universe.dev/'))
install.packages(c("BPCells", "presto", "glmGamPoi"))

We also recommend installing these additional packages, which are used in our vignettes, and enhance the functionality of Seurat:

Signac: analysis of single-cell chromatin data
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

# Install the remotes package
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
install.packages('Signac')
remotes::install_github("satijalab/seurat-data", quiet = TRUE)
remotes::install_github("satijalab/azimuth", quiet = TRUE)
remotes::install_github("satijalab/seurat-wrappers", quiet = TRUE)

Install previous versions of Seurat

Install Seurat v4

Seurat v4.4.0 can be installed with the following commands:

remotes::install_version("SeuratObject", "4.1.4", repos = c("https://satijalab.r-universe.dev", getOption("repos")))
remotes::install_version("Seurat", "4.4.0", repos = c("https://satijalab.r-universe.dev", getOption("repos")))

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:

# Install the remotes package 
install.packages('remotes')
# Replace 'X.X.X' with your desired version
remotes::install_version(package = 'Seurat', version = package_version('X.X.X'))

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)

Docker

We provide docker images for Seurat via dockerhub.

To pull the latest image from the command line:

docker pull satijalab/seurat:latest

To use as a base image in a new Dockerfile: