Source data for publication "A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and 'bad apple' effect on clinical trajectory" in Journal of Hepatology

Processed genomic and transcriptomic data for the publication https://doi.org/10.1016/j.jhep.2024.05.017.

cnv_segmentation.tsv: CNV segmentation file from Sequenza.

cnv_arm.tsv: Significant arm level CNV events called by GISTIC, from broad_values_by_arm.txt file.

cnv_gene.tsv: Gene level CNV events called by GISTIC, from all_threshold_by_genes.txt file. 

RNA_raw_counts.tsv: Raw RNA-seq read counts from featureCounts.

snv_indel.tsv: All SNV and Indel called with annotation from Funcotator.