REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Tumor tissue from participants in the CheckMate 038 clinical trial	CheckMate 038	CheckMate-038 clinical trial (NCT01621490) https://clinicaltrials.gov/ct2/show/results/NCT01621490
Deposited Data
Whole exome sequence data	This paper	EGAS00001004548
RNA sequencing data	This paper	EGAS00001004545
Software and Algorithms
VariantDx	Jones et al.47	N/A
ImmunoSelect-R	Personal Genome Diagnostics	N/A
MHCnuggets	Shao et al.48	https://github.com/KarchinLab/mhcnuggets
deconstructSigs	Rosenthal50	https://github.com/raerose01/deconstructSigs
SCHISM	Niknafs et al.51	https://github.com/KarchinLab/SCHISM
OptiType	Szolek et al.52	https://github.com/FRED-2/OptiType
xHLA	Xie et al.53	https://github.com/humanlongevity/HLA
SOAP-HLA	Cao et al.54	https://github.com/adefelicibus/soap-hla
POLYSOLVER	Shukla et al.55	https://software.broadinstitute.org/cancer/cga/polysolver
LOHHLA	McGranahan et al.56	https://bitbucket.org/mcgranahanlab/lohhla/src/master/
Trimmomatic	Bolger et al.57	http://www.usadellab.org/cms/index.php?page=trimmomatic
STAR	Dobin et al.58	https://github.com/alexdobin/STAR
Picard Tools	Broad Institute	https://broadinstitute.github.io/picard/
RSEM	Li and Dewey59	https://github.com/deweylab/RSEM
STAR-Fusion	Haas et al.60	https://github.com/STAR-Fusion/STAR-Fusion
CIBERSORT	Newman et al.32	https://cibersort.stanford.edu/
TIDE	Fu et al.61	http://tide.dfci.harvard.edu/
TRUST	Hu et al.33	https://github.com/liulab-dfci/TRUST4
MiXCR	Bolotin et al.63	https://github.com/milaboratory/mixcr
brms	Burkner64	https://github.com/paul-buerkner/brms
randomForest		https://cran.rstudio.com/web/packages/randomForest/
caret		https://cran.r-project.org/web/packages/caret/
ROCR		https://cran.r-project.org/web/packages/ROCR/
survminer		https://github.com/kassambara/survminer
survival		https://github.com/therneau/survival
coin		http://coin.r-forge.r-project.org
SPSS	IBM	N/A
R	R Core Team	https://www.r-project.org/