There is I've made available 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.
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- 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:
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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Unfortunately, the packages required to run Seurat on TACC are either out-of-date or not installed.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.