Introduction | Quickstart | Getting started | PBMC dataset | Loading the data | Profiling the soup | Adding extra meta data to the SoupChannel object | Visual sanity checks | Estimating the contamination fraction | Manually specifying the contamination fraction | Genes to estimate the contamination fraction | The automated method | The manual way | Picking soup specific genes | Estimating non-expressing cells | Calculating the contamination fraction | Correcting expression profile | Investigating changes in expression | Visualising expression distribution | Integrating with downstream tools | Loading into Seurat