REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
RNeasy Mini Kit	QIAGEN	Cat# 74104
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina	New England Biolabs	Cat# E7765
SureSelect XT Reagent Kit (Human All Exon V7)	Agilent	Cat# 232859
Deposited data
Raw total RNA-seq and whole exome sequencing data	This paper; dbGaP	dbGaP: phs003074.v1.p1
Processed data	This paper; dbGap	dbGaP: phs003074.v1.p1
Code for analysis of raw and processed data	This paper; Figshare	Figshare: https://doi.org/10.6084/m9.figshare.22595983
TCGA HTSeq – Counts files	Genomic Data Commons Data Portal	RRID: SCR_014514
TCGA survival data	cBioPortal	RRID: SCR_014555
MSigDB Hallmark v7.4 and C8 v7.2 modules	Molecular Signatures Database	RRID: SCR_016863
Molecular subclasses identified in previous studies	Candia et al., 202045	Supplementary Data 7; https://doi.org/10.1038/s41467-020-18186-1
Software and algorithms
CCBR Pipeliner	GitHub	RRID: SCR_002630
DRAGEN	Illumina	RRID: SCR_010233
survriskpred R package v0.2	BRBArrayTools	RRID: SCR_010938
ConsensusClusterPlus v1.56.0	Bioconductor	RRID: SCR_016954
ssGSEA2.0	Broad Institute	RRID: SCR_016863
CIBERSORTx	Stanford University	RRID: SCR_016955
Limma v3.48.3	Bioconductor	RRID: SCR_010943
Maftools v2.8.5	Bioconductor	RRID: SCR_006442
Other
NCI-CLARITY study website	This paper	https://ccr.cancer.gov/liver-cancer-program/nci-clarity-study