ImmunogenicityBenchmarking

Here, we proviide data and scripts to generate main figures in the manuscript.

Figure 1: Model Benchmarking

• OTB_Test_Models_CoV_2.rmd generates Figs 1A-B, as well as corresponding supplementary panels for S1.
• OTB_Test_Models_NEOAG_GBM.rmd generates Fig 1C as well as panels from supplementary S2.
• OTB_Test_Models_NEOAG_TESLA.rmd generates Fig 1D as well as panels from supplementary S3.

Figure 2: Differences in features associated with pathogen vs. cancer peptide immunogenicity

• Problems_Diff_Features_Path_Cancer_6_1.rmd generates panels from Figure 2.

Figure 3

• CrossHLA_Variation.rmd generates panels from Figure 3.

Extended Data

• Key datasets are supplied with the manuscript as supplementary data files. Additionally, they can be located in this repository in folder 'ExtendedData/'