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: .. image:: _static/gui/scouts_main_page_start.png :scale: 50% :alt: SCOUTS-violins main window :align: center 1) Choose your input data 2) Choose your sample names - `explanation here <./howscoutsworks.html#about-sample-names>`_ 3) Choose whether to gate samples and analyse other outlier populations - `explanation here <./howscoutsworks.html#gating-window>`_ 4) Choose how to perform outlier selection - `explanation here <./howscoutsworks.html#main-window>`_ 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: .. image:: _static/gui/scouts_violins_main_page_start.png :scale: 50% :alt: SCOUTS-violins main window :align: center 1) Choose your input data (same input file used for SCOUTS + SCOUTS output folder) 2) Choose your sample names - `explanation here <./howscoutsviolinsworks.html#main-window>`_ 3) Choose plot parameters 4) Plot your data