This repository holds code behind the article "A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary" by Conway, Pearce, Clipson et al, published in Nature Communications. This contains the code and data required to regenerate all the figures in the paper. The code is structured as follows: figure_inputs: Inputs required to generate the figures. Some of these are generated as part of the classifier generation/application process, some are additional clinical data. figure_generation: RMarkdown reports to generate the figures in the paper, given all the inputs in figures_inputs. These are separate RMarkdown files, and should be self-contained, and are able to be ran directly based on the files within `figure_inputs`. They may be ran in any order, except that CUP_mutation_analysis should be ran after CUPiD_cfDNA_application. The code will generate outputs in two folders, one called output and one called source_data; these are provided here for completeness. The source_data folder contains data for Nature Communications Source Data files, including data behind the ROC curves that are too large to be included there, while the output folder generates supplementary data tables and copies of the plots. Data and code to generate the classifier is available upon request from https://zenodo.org/uploads/10678015.