Introduction | Quick Start | Installation | Short Demo | Working with the SpatialExperiment class | Running Speed | Situations you should think twice about before applying SpotClean | Recommended applications | Detailed Steps | Load count matrix and slide information from 10x Space Ranger output | Create the slide object | Visualize the slide object | Decontaminate the data | Estimate contamination levels in observed data | ARC score | Convert to Seurat object for downstream analyses | Session Information | Citation

Introduction | Quick Start | Installation | All-in-one function | Running Speed | Saving a sparse matrix to 10x format | Detailed Steps | Read count matrix from 10x output raw data | Choose an appropriate background cutoff | Run CB2 to distinguish real cells from empty droplets | Extract real cell matrix | Downstream analysis | Session Information | Citation