RadioGx

DOI: 10.18129/B9.bioc.RadioGx    

This is the development version of RadioGx; to use it, please install the devel version of Bioconductor.

Analysis of Large-Scale Radio-Genomic Data

Bioconductor version: Development (3.12)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 0.99.10
In Bioconductor since BioC 3.12 (R-4.0)
License GPL-3
Depends R (>= 4.0), 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
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_0.99.10.tar.gz
Windows Binary RadioGx_0.99.10.zip
macOS 10.13 (High Sierra) RadioGx_0.99.10.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

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