GDSC based models for drug response prediction (Genome Biology, 2014) Note, the original link to this posted in the paper no longer works as the server hosting it at University of Chicago was disabled. The original webpage, code and data are mirrored in their entirety here: http://geeleherlab.org/cgpPrediction/
BioconductorBuntu (Bioinformatics, 2009): BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. Live CD and instructions.
GLDS (Genome Biology, 2016) An R package for improving the discovery of biomarkers in high-throughput drug screening data. This package, documentation and some use-cases are available on GitHub: https://github.com/paulgeeleher/glds
Consistency in Large Pharmacogenomic Studies (Nature, 2016) Our code and instructions are available on GitHub: https://github.com/paulgeeleher/nature_bca
IDWAS (Genome Research, 2017) This R package for implementing the imputed drug wide associations study strategy is available on GitHub: https://github.com/paulgeeleher/idwas
pRRophetic2 (Genome Research, 2017) An update to the pRRophetic R package, released with this updated paper is available on GitHub: https://github.com/paulgeeleher/pRRophetic2