Biomarkers Associated With Therapeutic Outcomes (BAWTO) In Prostate Cancer

Scripts and gists for creating/analyzing data synthesized from prostate cancer clinical trial publications.

Three sysrev projects were created for this analysis:

1. sysrev.com/p/63101: screening project for clinicaltrials.gov metadata
2. sysrev.com/p/68027: screening project for pubmed abstracts
3. sysrev.com/p/70431: pubmed data extraction project

Directory structure

• /figures - Publication figures
• /setup-scripts - Scripts to set up / analyze sysrev projects
  • /1. find-ctgov-trials.rmd
    A notebook to populate sysrev.com/p/63101 w/ mCRPC biomaker clinical trials from clinicaltrials.gov.
  • /2. big-analysis-notebook/big-analysis-notebook.rmd A notebook to analyze all sysrev data. Some dependencies are broken, results are stored in ./cache.image
• /figure-scripts scripts to build each publication image
  • fig1-prisma.R - prisma diagram for every project
  • fig2-timeline.R - clinical trial timelines
  • fig3-heatmap.Rmd - heatmap shows which trials use which biomarkers
  • fig4-HR-treemap.R - plotly treemap for hazard ratios
  • fig5-psa-forest.R - forest plot for PSA and PFS metrics
  • fig6-adverse-event.R - adverse event conditional distribution plots
  • fig7-models.Rmd - model based partitioning
• /cache.image - some of the dependencies in the big-analysis-notebook are broken. This cache was created to make image generation in figure-scripts easily reproducible.