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CoreGx

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


Bioconductor version: Release (3.18)

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

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

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CoreGx")

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

Documentation

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

browseVignettes("CoreGx")
CoreGx: Class and Function Abstractions HTML R Script
The TreatmentResponseExperiment Class HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Pharmacogenomics, Software, Survival
Version 2.6.0
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
URL
See More
Suggests pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat
Linking To
Enhances
Depends On Me PharmacoGx, RadioGx, ToxicoGx
Imports Me gDRimport, PDATK
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CoreGx_2.6.0.tar.gz
Windows Binary CoreGx_2.6.0.zip (64-bit only)
macOS Binary (x86_64) CoreGx_2.6.0.tgz
macOS Binary (arm64) CoreGx_2.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CoreGx
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CoreGx
Bioc Package Browser https://code.bioconductor.org/browse/CoreGx/
Package Short Url https://bioconductor.org/packages/CoreGx/
Package Downloads Report Download Stats