Package: RadioGx
Type: Package
Title: Analysis of Large-Scale Radio-Genomic Data
Version: 2.6.0
Date: 2023-04-19
Authors@R: c(
  person("Venkata","Manem", email = "mail2mvskumar@gmail.com",
    role = c("aut")),
  person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca",
    role = c("aut")),
  person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca",
    role = c("aut")),
  person("Meghan","Lambie", email = "megan.lambie@mail.utoronto.ca",
    role = c("aut")),
  person("Christopher","Eeles", email = "christopher.eeles@uhnresearch.ca",
    role = c("aut")),
  person("Scott", "Bratman", email = "scott.bratman@rmp.uhn.ca",
    role = c("aut")),
  person("Jermiah", "Joseph", email = "jermiah.joseph@uhn.ca",
    role = c("aut")),  
  person("Benjamin","Haibe-Kains", email = "benjamin.haibe.kains@utoronto.ca",
    role = c("aut","cre"))
  )
Description: 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) <doi:10.1101/449793>.
License: GPL-3
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
Encoding: UTF-8
LazyData: true
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
Suggests: rmarkdown, BiocStyle, knitr, pander, markdown
biocViews: Software, Pharmacogenetics, QualityControl, Survival,
        Pharmacogenomics, Classification
RoxygenNote: 7.2.3
Collate: 'OERmodel.R' 'RadioSet-class.R' 'RadioSet-accessors.R'
        'computeAUC.R' 'computeD10.R' 'computeSF2.R'
        'computeSensitivity.R' 'datasets.R' 'doseResponseCurve.R'
        'downloadRSet.R' 'geneDrugSensitivity.R' 'linearQuadratic.R'
        'linearQuadraticInv.R' 'linearQuadraticModel.R'
        'makeGrittyGuess.R' 'plotCurve.R' 'radSensitivitySig.R'
        'rankGeneRadSensitivity.R' 'signatureClass.R'
        'subsetTo-methods.R' 'summarizeMolecularProfiles-methods.R'
        'summarizeSensitivityProfiles-methods.R'
        'updateObject-methods.R' 'utilities.R' 'zzz.R'
git_url: https://git.bioconductor.org/packages/RadioGx
git_branch: RELEASE_3_18
git_last_commit: ea703e3
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 22:36:14 UTC; biocbuild
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@utoronto.ca>
Built: R 4.3.2; ; 2023-12-10 18:45:00 UTC; unix
