This workshop will introduce users to the CoreGx and PharmacoGx R packages, which are useful tools for pharmacogenomic modelling to discover biomarkers of treatment response in cancer model systems. PharmacoGx specifically focuses on drug sensitivity experiments in cancer cell lines, which will be the major focus of this workshop. Additional infrastructure from our lab includes ToxicoGx for toxicogenomics in healthy human cell-lines, RadioGx for radiogenomics in cancer cell-lines and Xeva for pharmacogenomics in patient derived xenograph (PDX) murine models.
Participants will learn the fundamentals of using CoreGx and PharmacoGx to create a PharmacoSet—an integrative container for the storage, analysis and visualization of pharmacogenomic experiments. Particular focus will be placed on newly developed support for storing, analyzing and visualizing drug combination sensitivity experiments and correlating results therefrom for with multi-omic molecular profiles to discover biomarkers of drug sensitivity or resistance.
Participants expected to have the following required packages installed on their machines to be able to run the commands along with the instructors. PharmacoGx, synergyfinder from Bioconductor, data.table from CRAN.
For a 1.5-hr workshop:
|Introduction to CoreGx and PharmacoGx||5m|
|Overview of Data Structures||15m|
|How TRE Support Drug Combinations Data Analysis||10m|
|Using Data Mapper to build a Drug Combo PharmacoSet.||10m|
|Dose Response Models and Drug Sensitivity measures||10m|
|Drug Combination Synergy Models||10m|
|Introduction to Resources for Biomarker Validation||5m|