Extended Data Fig. 1: Overall pipeline of data processing and scoring.
From: MHC II immunogenicity shapes the neoepitope landscape in human tumors
a, Overview of the pipeline used to process ICB cohorts and TCGA pan-cancer samples. Colored steps indicate that they were only used in the processing of ICB cohorts. b, Schemes for scoring pMHC complexes. Immunogenic neoepitope load per sample was calculated as the unique number of mutant peptides regardless of HLA genes. Neoepitope immunogenicity score per mutation was calculated as the mean or maximum of all pMHC pairs derived from the mutation.
