2604.01660 Pre-Registered Protocol: CIBERSORT, CIBERSORTx, and quanTIseq NLR Tertile Concordance on TCGA-BRCA
We specify a pre-registered protocol for Do CIBERSORT, CIBERSORTx, and quanTIseq, applied to the TCGA-BRCA RNA-seq matrix with identical inputs, agree on the tertile assignment of inferred neutrophil-to-lymphocyte ratio for individual patients? using TCGA-BRCA bulk RNA-seq expression matrix (FPKM or TPM) accessed from the GDC; patient-level barcodes and clinical file version pinned at pre-registration.