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install_v5.Rmd
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---
title: "Installation Instructions for Seurat"
output: html_document
---
To install Seurat, [R](https://www.r-project.org/) version 4.0 or greater is required. We also recommend installing [R Studio](https://www.rstudio.com/).
# {#id .class width=60 height=60} Seurat 5: Install from CRAN
Seurat is available on [CRAN](https://cran.r-project.org/package=Seurat) for all platforms. To install, run:
```{r, eval = FALSE}
# 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](https://github.com/immunogenomics/presto) (Korunsky/Raychaudhari labs), [BPCells](https://github.com/bnprks/BPCells) (Greenleaf Lab), and [glmGamPoi](https://github.com/const-ae/glmGamPoi) (Huber Lab). We recommend users install these along with users:
```{r, eval = FALSE}
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](https://github.com/stuart-lab/signac): analysis of single-cell chromatin data
* [SeuratData](https://github.com/satijalab/seurat-data): automatically load datasets pre-packaged as Seurat objects
* [Azimuth](https://github.com/satijalab/azimuth): local annotation of scRNA-seq and scATAC-seq queries across multiple organs and tissues
* [SeuratWrappers](https://github.com/satijalab/seurat-wrappers): enables use of additional integration and differential expression methods
```{r additional, eval=FALSE}
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 command:
```{r eval = FALSE}
install.packages('Seurat', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org'))
```
## 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:
```{r eval = FALSE}
# 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](https://github.com/satijalab/seurat/releases) and [install from the tarball](https://stackoverflow.com/questions/4739837/how-do-i-install-an-r-package-from-the-source-tarball-on-windows).
# Install the development version of Seurat
Install the development version of Seurat - directly from [GitHub](https://github.com/satijalab/seurat/tree/develop).
```{r eval = FALSE}
# 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](https://hub.docker.com/r/satijalab/seurat).
To pull the latest image from the command line:
```sh
docker pull satijalab/seurat:latest
```
To use as a base image in a new Dockerfile:
```sh
FROM satijalab/seurat:latest
```