Video Tutorial 
==============

This section will include access to a test datasest to learn how to use STEGO.R. 

This will include the video tutorials. 

Datasets
--------

Tutorial directory (https://zenodo.org/records/12665808) that contains the melanoma dataset with the lymph node and tumor single cell sample. 


The T cell atlas V2 (https://zenodo.org/records/12569981) will be used to demonstrate some of the functionality in Step 4. Analysis and post-analysis section. 

Quality control (Steps 1 to 3)
------------------------------

If you already have an .rds seurat object, and the TCR data was processed with scRepertoire proceed to Step 3e. to reformat the meta-data and then step 3c (annotation) and 3d (option).

STEP 1. 
^^^^^^^^

.. youtube:: aRB31LTj_VM
   :width: 640
   :height: 360


STEP 2. 
^^^^^^^^


STEP 3a. 
^^^^^^^^

STEP 3b. 
^^^^^^^^

STEP 3c. 
^^^^^^^^



- Why use semi-supervised annotations? 
- What are the available annotation models in STEGO.R?
- How to do a custom annotation? 

STEP 3d. 
^^^^^^^^



STEP 3e. 
^^^^^^^^






Analysis 
-----------