Software/Code

More information available on our labs St Jude Homepage!

Guiding Image Spatial Transcriptomics (GIST) (bioRxiv, 2021 – in review) The R package associated with this paper is available here: https://github.com/asifzubair/GIST Additional code is available here: https://github.com/asifzubair/GIST-paper

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: https://osf.io/pzke4/

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: https://github.com/paulgeeleher/cancerEqtls and the data to reproduce all results have been posted to Open Science Framework: https://osf.io/z7uyp/

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

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 The scripts to reproduce the analyses in the associated paper are available on Open Science Framework: https://osf.io/pwm4z/

Consistency in Large Pharmacogenomic Studies (Nature, 2016) Our code and instructions are available on GitHub: https://github.com/paulgeeleher/nature_bca

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 Code and data to reproduce the analyses in the paper are available on Zenodo: https://zenodo.org/record/60668

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.