thymus: the MHC class II arm lands -- 1,488 I-Ab thymic ligands

expression/SOURCES.md: the prose still said two sources

thymus + ligandome: the NOD tissue labels, settled by measurement

expression: GTEx has no thymus, so add the HPA consensus arm

expression: the mouse normal-tissue reference, and the thymus slice of it

thymus + ligandome: the mouse side, from deposits that needed no reprocessing

immunogenicity: the MHC class-II corpus the shipped class-II model is fitted on

neoantigens: the rest of the Sahin TNBC supplementary, processed

immunogenicity: deposit the staged IEDB export, the root of the provenance chain

immunogenicity: legacy arms, and species keyed on the restricting allele

immunogenicity: rebuild from the full IEDB export, with an allele for every record

neoantigens: the Sahin TNBC vaccine cohort (Nature 2025, s41586-025-10004-2)

SOURCES.md for every tracked directory, and drop the column nobody could define

Keep the MixMHCpred3 comparison material off the Hub

Split neoantigens from immunogenicity; add per-directory SOURCES with verified citations and audits

neoantigens/: the tested screens at epitope resolution

expression: GTEx per-tissue and TCGA per-tumour-type reference table

Add NCI complete neoantigen screen (iScience 2022 S6) as an immunogenicity variant

DESCRIPTION: document neoag_tested_{mmu,hsa} + flag 6186 mouse CEDAR rows mislabelled as human

Add neoag_tested_hsa: 717 HLA-restricted rows from the same IEDB mouse export (HLA-Tg mice + human hosts)

Add neoag_tested_mmu: 1977 murine tested neo-epitopes from IEDB (mhc_species=MusMusculus)

Publish TCGA neoantigens; add data-catalog infographic

thymus: add human thymic self-peptidome (source #1 refill)

data(proteome): add 16 bacterial + viral reference proteomes

neoag: primary datasets take precedence over CEDAR/Neopep; trim blank cols from iedb_labeled

DESCRIPTION: label iedb_labeled as the ipred training set (#7)

Rework #9 into workhorse neoag DB (tested + candidates) + HLA population freqs

Add v1 data compendium: immunogenicity labels/benchmarks + similarity references

Add pMHC dataset: epitope-MHC binding from IEDB

initial commit