This repository is an accompaniment to the ExoMeth manuscript published in The Prostate titled "Developing a multivariable risk model integrating urinary cell DNA methylation & cell-free RNA data for the detection of significant prostate cancer".
Great care has been taken throughout this work to ensure reproducibility. As such, all code required to quantitatively reproduce the analyses presented can be found here, including the RMarkdown file to produce the final formatted manuscript as submitted for peer review. For those lacking computational resources or the suitable rights over their environment this project has been set up with a Binder instance and RStudio Server.
This repository is the un-reviewed development version that I continure to work on and use for PRs to the archival version on the UEA Cancer Genetics page.
Multiple options exist for those interested in reproducing and investigating these analyses:
For those simply wanting to reproduce the analysis within their own environments this repo can be cloned, all dependencies installed by running install.R and the final document rendered by sourcing Render_Manuscript.R or by going through the RMarkdown document chunk by chunk.
For those wanting a less in-depth approach this project has been set up within a Binder environnment that can be spun up, requiring no dependencies to be installed on your machine. Please do be aware that the Binder instances are quite slow and several portions of the resampling loops can take quite some time to run!
