In this repository you will find scripts that help you filter, analyze and visualize single cell data using various R packages, such as 'Seurat', 'SCDE', 'scPred', 'harmony' etc.
The scripts are written for use with single cell UMI-based transcriptomic data, and were tested in datasets ranging from ~1000-150.000 gut mucosal (T-)cells from adapted smartseq2 protocols and 10x genomics v3 protocols.
See
http://satijalab.org/ # for sample data and tutorials
http://satijalab.org/seurat/visualization_vignette.html#interactive-plotting-features # for visualization tips