CoreGx

DOI: 10.18129/B9.bioc.CoreGx  

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

Bioconductor version: Release (3.17)

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>

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")

 

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

Details

biocViews	Classification, Pharmacogenomics, Software, Survival
Version	2.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 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
LinkingTo
Suggests	pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat
SystemRequirements
Enhances
URL
Depends On Me	PharmacoGx, RadioGx, ToxicoGx
Imports Me	PDATK
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CoreGx_2.4.0.tar.gz
Windows Binary	CoreGx_2.4.0.zip (64-bit only)
macOS Binary (x86_64)	CoreGx_2.4.0.tgz
macOS Binary (arm64)	CoreGx_2.4.0.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
Old Source Packages for BioC 3.17	Source Archive