RadioGx

DOI: 10.18129/B9.bioc.RadioGx    

Analysis of Large-Scale Radio-Genomic Data

Bioconductor version: Release (3.13)

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], Benjamin Haibe-Kains [aut, cre]

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	RadioGx: An R Package for Analysis of Large Radiogenomic Datasets
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Pharmacogenetics, Pharmacogenomics, QualityControl, Software, Survival
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.1), CoreGx
Imports	SummarizedExperiment, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader
LinkingTo
Suggests	rmarkdown, BiocStyle, knitr, pander, markdown
SystemRequirements
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_1.2.0.tar.gz
Windows Binary	RadioGx_1.2.0.zip
macOS 10.13 (High Sierra)	RadioGx_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RadioGx
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RadioGx
Package Short Url	https://bioconductor.org/packages/RadioGx/
Package Downloads Report	Download Stats