CoreGx

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

Bioconductor version: Release (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 utoronto.ca>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Pharmacogenomics, Software, Survival
Version	2.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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
System Requirements
URL

Suggests	pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat
Linking To
Enhances
Depends On Me	PharmacoGx, RadioGx, ToxicoGx
Imports Me	gDRimport
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_2.10.0.tar.gz
Windows Binary (x86_64)	CoreGx_2.10.0.zip
macOS Binary (x86_64)	CoreGx_2.10.0.tgz
macOS Binary (arm64)	CoreGx_2.10.0.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