Demo datasets for the protocol to identify shared transcriptional risks between diseases and compounds predicted to result in mutual benefit

We present a computational protocol (https://github.com/ghbore/protocol-cancer-cvd-similarity), implemented as a Snakemake workflow, that was used in previous works (Gao et al., 2022; Baylis et al., 2023). This protocol allows researchers to identify shared transcriptional processes that drive disease and to screen existing compounds for mutual benefit. The protocol also includes a description of the pharmacovigilance study design used to validate the effect of novel compounds using electronic health records, where applicable. This repository bundles the datasets used in previous works as an example to run through the Snakemake workflow. These datasets include the TCGA cancer dataset, the STARNET and BiKE CVD datasets, and other dependent resources.