Package: RadioGx 2.16.0

Benjamin Haibe-Kains

RadioGx: Analysis of Large-Scale Radio-Genomic Data

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>.

Authors: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]

RadioGx_2.16.0.tar.gz
RadioGx_2.16.0.zip(r-4.7)RadioGx_2.16.0.zip(r-4.6)RadioGx_2.16.0.zip(r-4.5)
RadioGx_2.16.0.tgz(r-4.6-any)RadioGx_2.16.0.tgz(r-4.5-any)
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RadioGx_2.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RadioGx/json (API)
NEWS

# Install 'RadioGx' in R:
install.packages('RadioGx', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:RadioGx-2.17.0(bioc 3.24)RadioGx-2.16.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarepharmacogeneticsqualitycontrolsurvivalpharmacogenomicsclassification

4.18 score 15 scripts 450 downloads 1 mentions 66 exports 133 dependencies

Last updated from:1b308e0403 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE213
linux-devel-x86_64OK430
source / vignettesOK279
linux-release-x86_64OK407
macos-release-arm64OK198
macos-oldrel-arm64OK177
windows-develOK289
windows-releaseOK262
windows-oldrelOK322
wasm-releaseOK169

Exports:.convertRsetMolecularProfilesToSEannotationannotation<-availableRSetscheckRSetStructurecomputeAUCcomputeD10computeSF2curationcuration<-datasetTypedatasetType<-dateCreateddateCreated<-doseResponseCurvedownloadRSetfeatureInfofeatureInfo<-fNamesfNames<-linearQuadraticModelmDataNamesmDataNames<-molecularProfilesmolecularProfiles<-molecularProfilesSlotmolecularProfilesSlot<-namename<-pertNumberpertNumber<-phenoInfophenoInfo<-plotCurveradiationInforadiationInfo<-radiationTypesradiationTypes<-RadioSetRadioSigradSensitivitySigsampleInfosampleInfo<-sampleNamessampleNames<-sensitivityInfosensitivityInfo<-sensitivityMeasuressensitivityProfilessensitivityProfiles<-sensitivityRawsensitivityRaw<-sensNumbersensNumber<-showshowSigAnnotsubsetTosummarizeMolecularProfilessummarizeSensitivityProfilestreatmentInfotreatmentInfo<-treatmentNamestreatmentNames<-treatmentResponsetreatmentResponse<-updateObject

Dependencies:abindassertthatbackportsbase64encbenchBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbitopsbslibBumpyMatrixcachemcaToolscelestialcheckmatecliclustercodetoolscommonmarkCoreGxcowplotcpp11crayoncrosstalkdata.tableDelayedArraydigestdownloaderdplyrDTevaluatefarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvigraphIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalsamagicaxismagrittrmapprojmapsmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentNISTunitsotelpianopillarpkgconfigplotrixplyrpracmaprofmempromisespurrrR6RANNrappdirsRColorBrewerRcpprelationsreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosetsshinyshinydashboardshinyjsslamsmsnowSnowballCsourcetoolsSparseArraystatmodstringistringrSummarizedExperimenttibbletidyrtidyselecttinytexutf8vctrsviridisLitevisNetworkwithrxfunxtableXVectoryaml

RadioGx: An R Package for Analysis of Large Radiogenomic Datasets

Venkata Manem, Petr Smirnov, Ian Smith, Meghan Lambie, Christopher Eeles, Scott Bratman, Benjamin Haibe-Kains

Rendered fromRadioGx.Rmdusingknitr::knitron May 30 2026.

Last update: 2022-07-18
Started: 2020-03-31

Readme and manuals

Help Manual

Help pageTopics
`[`[,RadioSet,ANY,ANY,ANY-method
Return a table of RadioSets available for downloadavailableRSets
A function to verify the structure of a RadioSetcheckRSetStructure
Cleaveland_mut RadioSet subsettedclevelandSmall
computeAUC: computes AUCcomputeAUC
Compute D10computeD10
Compute SF2computeSF2
Get the dimensions of a RadioSetdim,RadioSet-method
Plot drug response curve of a given drug and a given cell for a list of rSets (objects of the RadioSet class).doseResponseCurve
Download a RadioSet objectdownloadRSet
Fit linear-quadratic curves to dose-response datalinearQuadraticModel
Plot radiation dose-response curveplotCurve
RadioSet constructorRadioSet
Accessing and modifying information in a `RadioSet`annotation annotation,RadioSet-method annotation<- annotation<-,RadioSet,list-method cellInfo cellInfo,RadioSet-method cellInfo<- cellInfo<-,RadioSet,data.frame-method cellName,RadioSet-method cellNames cellNames<- cellNames<-,RadioSet,list-method curation curation,RadioSet-method curation<- curation<-,RadioSet,list-method datasetType datasetType,RadioSet-method datasetType<- datasetType<-,RadioSet,character-method dateCreated dateCreated,RadioSet-method dateCreated<- dateCreated<-,RadioSet,character-method dateCreated<-,RadioSet-method featureInfo featureInfo,RadioSet-method featureInfo<- featureInfo<-,RadioSet,character,data.frame-method featureInfo<-,RadioSet,character,DataFrame-method fNames fNames,RadioSet,character-method fNames<- fNames<-,RadioSet,character,character-method mDataNames mDataNames,RadioSet-method mDataNames<- mDataNames<-,RadioSet,ANY-method mDataNames<-,RadioSet-method molecularProfiles molecularProfiles,RadioSet-method molecularProfiles<- molecularProfiles<-,RadioSet,character,character,matrix-method molecularProfiles<-,RadioSet,character,missing,matrix-method molecularProfiles<-,RadioSet,missing,missing,list-method molecularProfiles<-,RadioSet,missing,missing,MutliAssayExperiment-method molecularProfilesSlot molecularProfilesSlot,RadioSet-method molecularProfilesSlot<- molecularProfilesSlot<-,RadioSet,list-method molecularProfilesSlot<-,RadioSet,list_OR_MAE-method molecularProfilesSlot<-RadioSet,MultiAssayExperiment-method moleculerProfilesSlot,RadioSet-method name name,RadioSet-method name<- name<-,RadioSet,character-method name<-,RadioSet-method pertNumber pertNumber,RadioSet-method pertNumber<- pertNumber<-,RadioSet,array-method phenoInfo phenoInfo,RadioSet,character-method phenoInfo<- phenoInfo<-,RadioSet,character,data.frame-method phenoInfo<-,RadioSet,character,DataFrame-method radiationInfo radiationInfo<- radiationTypes radiationTypes<- RadioSet-accessors sampleInfo sampleInfo,RadioSet-method sampleInfo<- sampleInfo<-,RadioSet,data.frame-method sampleName,RadioSet-method sampleNames sampleNames,RadioSet-method sampleNames<- sampleNames<-,RadioSet,character-method sampleNames<-,RadioSet,list-method sensitivityInfo,RadioSet,character-method sensitivityInfo,RadioSet,missing-method sensitivityInfo,RadioSet-method sensitivityInfo<-,RadioSet,data.frame-method sensitivityInfo<-,RadioSet,missing,data.frame-method sensitivityMeasures,RadioSet-method sensitivityMeasures<-,RadioSet,character-method sensitivityProfiles,RadioSet-method sensitivityProfiles<-,RadioSet,data.frame-method sensitivityRaw,RadioSet-method sensitivityRaw<-,RadioSet,array-method sensitivitySlot sensitivitySlot<- sensitvityInfo<-,RadioSet,character,data.frame-method sensNumber sensNumber,RadioSet-method sensNumber<- sensNumber<-,RadioSet,matrix-method treamentResponse<-,RadioSet,list-method treatmentInfo treatmentInfo,RadioSet-method treatmentInfo<- treatmentInfo<-,RadioSet,data.frame-method treatmentNames treatmentNames,RadioSet-method treatmentNames<- treatmentNames<-,RadioSet,character-method treatmentResponse treatmentResponse,RadioSet-method treatmentResponse<- treatmentResponse<-,RadioSet,list_OR_LongTable-method treatmentResponse<-,RadioSet,LongTable-method
A Class to Contain RadioGenomic datasets together with their curations.RadioSet RadioSet-class
Radiation Signature Class ConstructorRadioSig
Creates a signature representing the association between gene expression (or other molecular profile) and radiation dose response, for use in radiation sensitivity analysis.radSensitivitySig
Show a RadioSetshow,RadioSet-method
Show RadioGx Signaturesshow,RadioSig-method
Show the Annotations of a signature objectshowSigAnnot,RadioSig-method
A function to subset a RadioSet to data containing only specified radiations, cells and genessubsetTo,RadioSet-method
Takes molecular data from a RadioSet, and summarises them into one entry per drugsummarizeMolecularProfiles,RadioSet-method
Takes the sensitivity data from a RadioSet, and summarises them into a drug vs cell line tablesummarizeSensitivityProfiles,RadioSet-method
Update the RadioSet class after changes in it struture or APIupdateObject,RadioSet-method