genome - analysis scripts for the whole genome sequencing data
transcriptome - analysis scripts for the RNA sequencing data
HD - analysis scripts for the spatial transcriptome (10X HD) data
stat and plot - compare samples from difference groups, plot graphs.
external dataset - compare with external datasets.
Please cite our paper if you find this work is helpful to your research. Zhang Z, Li H, Chen L, Lu T, Shentu X, Liu Y, Ji S, Qiu Z, Zou Y, Wen H, Han J, Jiang Z, Fan J, Li D, Mesropian A, Pinyol R, Llovet JM, Dong H, Ji Y, Hui L. Molecular insights into early malignant transition of hepatocellular carcinoma. bioRxiv [Preprint]. 2025 Apr 15:2025.04.14.648739. doi: 10.1101/2025.04.14.648739. PMID: 40321210; PMCID: PMC12047883.