The SysBioOncology/SPoTLIghT documentation is split into the following pages:
- Usage
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
- Modules
- Provides an in-depth overview of the different modules in the SPoTLIghT pipeline.
- Output
- An overview of the different results produced by the pipeline and how to interpret them.
- Building models
- How to build cell type models using TCGA datasets with FF slides.
- Examples
- Examples showcasing how to extract spatial features from H&E images using the built SKCM models provided with the repository.