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St. Jude Research
Geeleher Lab

Software & Code

  1. Guiding Image Spatial Transcriptomics (GIST)

    bioRxiv, 2021 [In review]

  2. 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.

  3. Methods for identifying cell-type-specific eQTLs from bulk tumor RNA-seq

    Genome Biology, 2018

  4. pRRophetic2

    Genome Research, 2017

    An update to the pRRophetic R package, released with this updated paper is available on GitHub.

  5. 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.

  6. Consistency in Large Pharmacogenomic Studies

    Nature, 2016

    Our code and instructions are available on GitHub.

  7. GLDS

    Genome Biology, 2016

    An R package for improving the discovery of biomarkers in high-throughput drug screening data.

  8. 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.

  9. 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.