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This is the development version of CoreGx; for the stable release version, see CoreGx.

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Bioconductor version: Development (3.20)

A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .

Author: Jermiah Joseph [aut], Petr Smirnov [aut], Ian Smith [aut], Christopher Eeles [aut], Feifei Li [aut], Benjamin Haibe-Kains [aut, cre]

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at>

Citation (from within R, enter citation("CoreGx")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CoreGx: Class and Function Abstractions HTML R Script
The TreatmentResponseExperiment Class HTML R Script
Reference Manual PDF


biocViews Classification, Pharmacogenomics, Software, Survival
Version 2.9.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 3)
Depends R (>= 4.1), BiocGenerics, SummarizedExperiment
Imports Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench
System Requirements
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Suggests pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat
Linking To
Depends On Me PharmacoGx, RadioGx, ToxicoGx
Imports Me gDRimport, PDATK
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package CoreGx_2.9.0.tar.gz
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macOS Binary (x86_64) CoreGx_2.9.0.tgz
macOS Binary (arm64) CoreGx_2.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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