RSG Turkey invites all its members to the workshop titled "Introduction to Single-cell RNA-seq Analysis using Seurat," which will be delivered by Ali Yavuz Çakır. The workshop will take place on September 23, 2024, from 10:00 AM to 3:00 PM. This is a great opportunity to learn how to work with single-cell RNA-seq data and master the analysis process.

Workshop content:

• Using the Seurat package
• Analysis of single-cell RNA-seq data
• Automatic cell type annotation for PBMC_10x_v2
• Integration of two datasets

We look forward to the participation of all our members!

Date: September 23, 2024

Time: 10:00 AM - 3:00 PM

To prepare for the workshop happening next Monday, please ensure you have completed the following:

Before You Start

Make sure to create a working directory and use an R script in Rstudio to type your command lines, as we covered in our previous workshop.

1. Installation Instructions for Seurat

R and RStudio Setup

• Seurat requires R version 4.0 or greater.
• We recommend installing RStudio.

Installing Seurat 5 from GitHub

Install devtools

This package is necessary to install some packages from GitHub.

if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")
}
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)

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:

Do you want to attempt to install these from sources?
y/n:

Install from Conda

To install this package run one of the following:

conda install bioconda::r-seurat
conda install bioconda/label/cf201901::r-seurat
conda install bioconda/label/gcc7::r-seurat

Install Seurat and SeuratData in R

The core packages for your workshop will be Seurat and SeuratData.

Install Seurat V5

if (!requireNamespace("Seurat", quietly = TRUE)) {
install.packages("Seurat")
}
# Install SeuratData
if (!requireNamespace("SeuratData", quietly = TRUE)) {
install.packages("SeuratData")
}

2. Install Additional Useful Packages

Data manipulation and visualization

• dplyr and tidyverse: for efficient data wrangling.

• ggplot2: for powerful and flexible data visualization.

if (!requireNamespace("dplyr", quietly = TRUE)) {
install.packages("dplyr")
}
if (!requireNamespace("tidyverse", quietly = TRUE)) {
install.packages("tidyverse")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
install.packages("ggplot2")
}

3. Verify Installation

After installing all the packages, it’s good practice to load them to ensure everything is working correctly. Load core packages

library(Seurat)

library(SeuratData)

Load data wrangling and visualization packages

library(dplyr)

library(ggplot2)