More information available on our labs St Jude Homepage!

Guiding Image Spatial Transcriptomics (GIST) (Nucleic Acids Research, 2022 – in review) The R package associated with this paper is available here.

Additional code is available here: and

Dataset alignment for drug repurposing (Nature Communications, 2021) The code used to discover CX-5461 as a candidate therapeutic for neuroblastoma is available on Open Science Framework:

Methods for identifying cell-type-specific eQTLs from bulk tumor RNA-seq (Genome Biology, 2018) The methods and analyses from this paper are on GitHub: and the data to reproduce all results have been posted to Open Science Framework:

pRRophetic2 (Genome Research, 2017) An update to the pRRophetic R package, released with this updated paper is available on GitHub:

IDWAS (Genome Research, 2017) This R package for implementing the imputed drug wide associations study strategy is available on GitHub: The scripts to reproduce the analyses in the associated paper are available on Open Science Framework:

Consistency in Large Pharmacogenomic Studies (Nature, 2016) Our code and instructions are available on GitHub:

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: Code and data to reproduce the analyses in the paper are available on Zenodo:

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:

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.