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)
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("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 | ||
| NEWS | Text |
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 |
| Linking To | |
| Suggests | pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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 |