RadioGx
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see RadioGx.
Analysis of Large-Scale Radio-Genomic Data
Bioconductor version: 3.19
Computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The 'RadioSet' class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. 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, references, as well as: Manem, V. et al (2018)
Author: Venkata Manem [aut], Petr Smirnov [aut], Ian Smith [aut], Meghan Lambie [aut], Christopher Eeles [aut], Scott Bratman [aut], Jermiah Joseph [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
citation("RadioGx")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RadioGx")
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("RadioGx")| RadioGx: An R Package for Analysis of Large Radiogenomic Datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Pharmacogenetics, Pharmacogenomics, QualityControl, Software, Survival |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), CoreGx |
| Imports | SummarizedExperiment, BiocGenerics, data.table, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, BiocStyle, knitr, pander, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RadioGx_2.8.0.tar.gz |
| Windows Binary (x86_64) | RadioGx_2.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | RadioGx_2.8.0.tgz |
| macOS Binary (arm64) | RadioGx_2.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RadioGx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RadioGx |
| Bioc Package Browser | https://code.bioconductor.org/browse/RadioGx/ |
| Package Short Url | https://bioconductor.org/packages/RadioGx/ |
| Package Downloads Report | Download Stats |