I've made available some publicly available data 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 (using variable features)
• Cluster the cells (using the selected number of dimensions)
• Find markers for each cluster
• Visualize the clusters using tSNE or UMAP
• Identify cells expressing genes of interest 
• Label clusters as cell types based on expression of known marker genes.

You can get the data and R script from stampede2 here:

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

The script: seuratTotalScript5k.R

The data: filtered_feature_bc_matrix

Unfortunately, the packages required to run Seurat on TACC  are either out-of-date or not installed. So, we are not going to run this script today.