REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Trolle Ligand Dataset	IEDB (Vita et al., 2019)	http://www.iedb.org/subID/1000685
HeLa RNA-Seq	GEO	GSM3899456
Abelin Ligand Dataset	Abelin et al. (Abelin et al., 2017)	Table S1
Abelin RNA-Seq	GEO	GSE93315
Pyke Ligand and Neoantigen Datasets	Pyke et al. (Pyke et al., 2021)	Tables S1 and S5
K562 RNA-Seq	Cancer Cell Line Encyclopedia (Ghandi et al., 2019)	CCLE_RNAseq_rsem_genes_tpm_20180929.txt.gz https://depmap.org/portal/download/api/download?file_name=ccle%2Fccle_2019%2FCCLE_RNAseq_rsem_genes_tpm_20180929.txt.gz&bucket=depmap-external-downloads
TCGA PANCAN RNA-Seq Dataset	TCGA	https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/EB%2B%2BAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz
NCI Dataset of Neoantigens	Parkhurst et al. (Parkhurst et al., 2019)	Table S3
Literature Dataset of Neoantigens	IEDB (Vita et al., 2019; Kosaloglu-Yalcin et al., 2021)	using the following filters: Epitope Structure: Linear Sequence, Included Related Structures: Only neoepitopes, Include Positive Assays, Include Negative Assays, No B cell assays, No MHC assays, MHC Restriction Type: Class I, Host: Homo sapiens (human), Organism: Homo sapiens (human) (ID:9606, human)
Tarke Dataset of SARS-CoV-2 Epitopes	Tarke et al. (Tarke et al., 2021)	Table S5
Peng Dataset of SARS-CoV-2 Epitopes	Peng et al. (Peng et al., 2020)	Table S2
SARS-CoV-2 Proteome	UniProt	UP000464024
SARS-CoV-2 RNA-Seq and Ribo-Seq data	GEO	GSE149973
SARS-CoV-2 Proteomic Dataset	Poran et al. (Poran et al., 2020)	Table S10
Software and algorithms
NetMHCpan 4.1	Reynisson et al. (Reynisson et al., 2020b)	http://tools.iedb.org/mhci/
IEDB	Vita et al. (Vita et al., 2019)	http://tools.iedb.org/mhci/
MHCFlurry	O’Donnell et al. (O’Donnell et al., 2020)	https://openvax.github.io/mhcflurry/intro.html
MixMHCPred	Gfeller et al. (Gfeller et al., 2018)	https://github.com/GfellerLab/MixMHCpred
HLAathena	Sarkizova et al. (Sarkizova et al., 2020)	http://hlathena.tools
R	R	https://www.r-project.org
Python	Python	https://www.python.org