Scripts mainly associated with the SAAV chapter in the manuscript entitled "Proteogenomics stratification of treatment naïve melanoma metastases associates the tumor microenvironment with disease progression and patient outcome".
- SpectrumAI_SpectraFunctions.R: the utility functions originally from https://github.com/yafeng/SpectrumAI/blob/master/Spectra_functions.R.
- SpectrumAI_customized.R: the script to validate PSMs of variant peptides; originally from https://github.com/yafeng/SpectrumAI/blob/master/SpectrumAI.R.
- Fig1A_heatmap.R: script for Figure 1A heatmap (heatmap of proposed melanoma subtypes)
- Suppl_Figure_SAAV_chapter_OmicCircos.R: script for the supplementary figures in the SAAV chapter.