This Github repository provides the code associated with the following manuscript: 

Shu, D.H., Ho, W.J., Kagohara, L.T. et al. Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma. Nat Immunol 25, 2110–2123 (2024). https://doi.org/10.1038/s41590-024-01992-w

Data for all analyses have been shared as described in the manuscript. IMC data files have been deposited and are available via Zenodo at https://doi.org/10.5281/zenodo.10020271. Processed bulk RNA sequencing and single-cell RNA/TCR/BCR sequencing data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus database under accession code GSE272348. Bulk TCR-β and IGH sequencing data are available from the Adaptive Biotechnologies ImmuneACCESS repository (https://clients.adaptivebiotech.com/pub/shu-2024-ni). All other data are present in the Article and its supplementary files or can be obtained from the corresponding authors upon reasonable request.

Numerical prefixes for R markdown files and the folder "2_IMC" indicate separate analyses included in the paper. The "2_IMC" folder should be used in association with IMC data files available on Zenodo to reproduce the results presented in the paper. Files with the prefix "sessionInfo" indicate the corresponding output of the R function sessionInfo for each script.