Drug-level effects dominate within-cell-line cancer drug prioritisation: data and code

Data and code accompanying a study of within-cell-line drug ranking by drug-response models. Using the published predictions of the DrEval benchmark on CTRPv2, the study compares rankings on the raw response with rankings after removal of drug-level and tissue–drug effects, and evaluates transfer to unseen cell lines of GDSC2 and GDSC1. The deposit contains the pre-specified and post hoc analysis protocols, the analysis scripts as executed, all reported outputs and figures, and the record of a reproduction in a clean environment from the deposited materials and the identified external data (of 727 output files compared with the reported outputs, 699 were byte-identical and 27 matched under documented comparison rules; the remaining one, a compressed table, was checked after decompression and its content matched the reference; none was different or missing). Third-party DrEval data (Zenodo record 21807175) are cited and not redistributed.