ABCmonster

We present companion materials for our paper titled Characterizing ABC-transporter substrate-likeness using a clean-slate genetic background. All code and data used in the paper is encapsulated inside an R package. The package can be installed by running the following commands within R:

if( !require(devtools) ) install.packages( "devtools" )
devtools::install_github( "labsyspharm/ABCmonster" )

The package provides several functions that simplify reproducibility of the analyses described in the paper. These functions are outlined in the Reference section. All other scripts are described across three vignettes:

  • Overview of raw data, where we describe the training data and present several unsupervised analyses;
  • Cross-validation, where we evaluate several prediction methods in a cross-validation setting;
  • and Prospective validation, where we describe novel drug sensitivity data that we collected on the ABC-16 strain and compare predictions made by the model against this data.

Funding

We gratefully acknowledge support by NIGMS Grant P50GM107618: the HMS Laboratory of Systems Pharmacology, by NIH Grant 1U54CA225088-01: Systems Pharmacology of Therapeutic and Adverse Responses to ImmuneCheckpoint and Small Molecule Drugs, and by the Canadian Excellence Research Chairs (CERC) Program (to FPR).