The standard Seurat scRNA downstream analysis pipeline

For more information: https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html

Parameters:

• minUMI: Minimum number of UMI counts for each cell (default: 1000)
• maxUMI: Maximum number of UMI counts for each cell (default: 10000)
• mitoRatio: Maximum mitochondrial contamination percentage for each cell (default: 5)
• varFeatures: The number of most variable genes (default: 2000, see Seurat tutorial)

Steps:

• Filter cells with low and high UMI counts
• Normalize, and find most variable genes
• Scale UMI counts, find top PCs and cluster cells with resolution=0.4, 0.6, 0.8, 1.0, 1.4 (see Seurat tutorial)
• Project clusters to UMAP

Output:

• Seurat object with resulting clusters
• h5ad file for Cellxgene and annotation
• UMAP of clusters
• UMAP of UMI counts
• UMI density plots of clusters
• Heatmap of marker genes (top 12)
• Table of markers genes (top 50)