RadioGx

This is the development version of RadioGx; for the stable release version, see RadioGx.

Analysis of Large-Scale Radio-Genomic Data

Bioconductor version: Development (3.18)

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 (from within R, enter citation("RadioGx")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	PDF
NEWS	Text

Details

biocViews	Classification, Pharmacogenetics, Pharmacogenomics, QualityControl, Software, Survival
Version	2.5.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 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
Linking To
Suggests	rmarkdown, BiocStyle, knitr, pander, markdown
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RadioGx_2.5.0.tar.gz
Windows Binary	RadioGx_2.5.0.zip (64-bit only)
macOS Binary (x86_64)	RadioGx_2.5.0.tgz
macOS Binary (arm64)	RadioGx_2.5.0.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