Intro to Seurat
Seurat is an R package that takes the output from Cell Ranger and other pipelines for QC, analysis, and visualization of single cell data.
Capabilities:
- Basics: preprocessing, QC, dimensional reduction, clustering, differential expression
- Multimodal analysis (e.g., paired scRNA-seq & scATAC-seq)
- Spatial datasets (transcriptomic or multiplexed imaging-based)
- Data integration (multiple sources of single cell data)
In this tutorial, we will use Seurat to analyze a dataset of 2,700 Peripheral Blood Mononuclear Cells (PBMCs) made publicly available by 10X Genomics.
The standard unsupervised clustering workflow includes QC and data filtration, calculation of high-variance genes, dimensional reduction, graph-based clustering, and the identification of cluster markers.