安装Seurat包
安装Seurat包
install.packages(‘Seurat‘)
library(‘Seurat‘)
packageVersion("Seurat")
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install.packages(c(‘dplyr‘,‘patchwork‘))
> BiocManager::install("Seurat",ask = F,update = F)
‘getOption("repos")‘ replaces Bioconductor standard repositories, see ‘?repositories‘ for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.10 (BiocManager 1.30.16), R 3.6.0 (2019-04-26)
Installing package(s) ‘Seurat‘
Warning message:
In .inet_warning(msg) :
package ‘Seurat’ is not available (for R version 3.6.0)
> install.packages(‘Seurat‘)
Warning in install.packages :
package ‘Seurat’ is not available (for R version 3.6.0)
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Installation Instructions for Seurat
Source:vignettes/install.Rmd
To install Seurat, R version 4.0 or greater is required. We also recommend installing R Studio.
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:
install.packages(‘remotes‘)remotes::install_version("Seurat", version = "3.2.3")
ERROR: dependencies ‘leiden‘, ‘lmtest‘, ‘png‘, ‘reticulate‘, ‘ROCR‘, ‘rsvd‘, ‘scattermore‘, ‘sctransform‘, ‘spatstat‘, ‘uwot‘ are not available for package ‘Seurat‘
install.packages(‘leiden‘)install.packages(‘lmtest‘)
install.packages(‘png‘)
install.packages(‘reticulate‘)
install.packages(‘ROCR‘)
install.packages(‘rsvd‘)
install.packages(‘scattermore‘)
install.packages(‘sctransform‘)
install.packages(‘spatstat‘)
install.packages(‘uwot‘)
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")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)Docker
We provide docker images for Seurat via dockerhub.
To pull the latest image from the command line:
docker pull satijalab/seurat:latestTo use as a base image in a new Dockerfile:
FROM satijalab/seurat:latest链接：https://www.jianshu.com/p/d4df73ff6a2e