Authors: Xiaochen Zhang, Ruiqing Zhu, Jiadong Mao, Kim-Anh Lê Cao, Saritha Kodikara, Daniel Rawlinson
| Audience | Prerequisites | Duration |
|---|---|---|
| Anyone | Install R & R Studio | ~ 10 min |
| Anyone | Install Seurat and SeuratData | ~ 30 min |
This repository includes material for a hands-on workshop 'Introduction to scRNA-seq analysis'. We show you how to use Seurat to analysis your own scRNA-seq data.
Install R first, then RStudio. Download the most recent version of R and RStudio using the links below:
Install the R packages (you will need R version > 4.0, preferably 4.2 to avoid most issues with the installation). Type the R command lines:
install.packages('Seurat')
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("satijalab/seurat-data", quiet = TRUE)
# then test if packages have been installed
library(Seurat)
library(SeuratData)
# And install the data
InstallData("pbmcsca")
data("pbmcsca")
pbmcsca <- UpdateSeuratObject(pbmcsca)
More details on the packages:
Click here to access the HTML workshop document.
Datasets are from the SeuratData package.