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A repository to house the code relevant to the project "Systematic Rational Identification of Sex-Linked Molecular Alterations and Therapies in Cancer." The repository contains R scripts used to process and analyze data and results. In our work, we identify cancer-specific and pan-cancer genomic differences between male and female patients. Then, we use Ingenuity Pathway Analysis (IPA) to discover pathways variably enriched in male and female tumors, lending insight into the biological processes that differ between both sexes. Finally, we use our genomic findings to identify drugs that work well in males, females, or both sexes.


Presents a simple and freely accessible software tool for identification of sex chromosome linked genes in species without an existing reference genome. This pipeline uses custom scripts together with external assembly, mapping and variant calling software. Given the resource-intensive nature of the computation, servers with high capacity are a requirement. Therefore, in order to keep this pipeline easily accessible and reproducible, linkyx was implemented in Galaxy – an open, web-based platform for data-intensive biomedical research.