Basic usage

The scouts package include two user interfaces:

• SCOUTS: used to select outliers in a population of single-cells.
• SCOUTS-violins (optional): used to visually inspect outliers selected by SCOUTS.

Using SCOUTS

This is a basic rundown of the interface when you start SCOUTS:

1. Choose your input data
2. Choose your sample names - explanation here
3. Choose whether to gate samples and analyse other outlier populations - explanation here
4. Choose how to perform outlier selection - explanation here
5. Choose how and where to save output
6. Run the program

Using SCOUTS-violins

This is a basic rundown of the interface when you start SCOUTS-violins:

1. Choose your input data (same input file used for SCOUTS + SCOUTS output folder)
2. Choose your sample names - explanation here
3. Choose plot parameters
4. Plot your data