CoreGx

DOI: 10.18129/B9.bioc.CoreGx    

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

Bioconductor version: Release (3.11)

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 'PharmaSet' 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], 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 "4.0") and enter:

if (!requireNamespace("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
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Pharmacogenomics, Software, Survival
Version 1.0.2
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports Biobase, S4Vectors, SummarizedExperiment, piano, BiocParallel, methods, stats, utils, graphics, grDevices, lsa
LinkingTo
Suggests pander, BiocStyle, rmarkdown, knitr
SystemRequirements
Enhances
URL
Depends On Me PharmacoGx
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CoreGx_1.0.2.tar.gz
Windows Binary CoreGx_1.0.2.zip
macOS 10.13 (High Sierra) CoreGx_1.0.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CoreGx
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CoreGx
Package Short Url https://bioconductor.org/packages/CoreGx/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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