There is some publicly available data available containing single cell RNA-Seq data for 5k immune cells as well as a script that runs the Seurat workflow to define cell-type clusters in this data.

The script does the following:

• Load Data and Create Seurat Object
• Normalize Data Using SCTransform and Regress out Genes Related to Cell Cycle

• Identify Highly Variable Features

• Scale the Data

• Select Dimensions using PCA
• Cluster the cells
• Find markers for each cluster
• Visualize the clusters using tSNE or UMAP

You can get the data and R script from ls5 here:

/work2/projects/BioITeam/projects/courses/rnaseq_course/day_5_single_cell_data

The script: seuratTotalScript5k.R

The data: filtered_feature_bc_matrix