CoreGx
This is the development version of CoreGx; for the stable release version, see CoreGx.
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Bioconductor version: Development (3.24)
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: 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("CoreGx")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 2.17.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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 |
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_2.17.0.tar.gz |
| Windows Binary (x86_64) | CoreGx_2.17.0.zip |
| macOS Binary (big-sur-x86_64) | CoreGx_2.17.0.tgz |
| macOS Binary (sonoma-arm64) | CoreGx_2.17.0.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 |