Package: RadioGx 2.17.0

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_2.17.0.tar.gz
RadioGx_2.17.0.zip(r-4.7)RadioGx_2.17.0.zip(r-4.6)RadioGx_2.17.0.zip(r-4.5)
RadioGx_2.17.0.tgz(r-4.6-any)RadioGx_2.17.0.tgz(r-4.5-any)
RadioGx_2.17.0.tar.gz(r-4.7-any)RadioGx_2.17.0.tar.gz(r-4.6-any)
RadioGx_2.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RadioGx/json (API)

# Install 'RadioGx' in R:

install.packages('RadioGx', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

clevelandSmall - Cleaveland_mut RadioSet subsetted

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.

software pharmacogenetics qualitycontrol survival pharmacogenomics classification

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

Last updated from:238a2e31ce. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	201
linux-devel-x86_64	OK	440
source / vignettes	OK	296
linux-release-x86_64	OK	420
macos-release-arm64	OK	209
macos-oldrel-arm64	OK	213
windows-devel	OK	329
windows-release	OK	325
windows-oldrel	OK	340
wasm-release	OK	158

Exports:.convertRsetMolecularProfilesToSE annotation annotation<-availableRSets checkRSetStructure computeAUC computeD10 computeSF2 curation curation<-datasetType datasetType<-dateCreated dateCreated<-doseResponseCurve downloadRSet featureInfo featureInfo<-fNames fNames<-linearQuadraticModel mDataNames mDataNames<-molecularProfiles molecularProfiles<-molecularProfilesSlot molecularProfilesSlot<-name name<-pertNumber pertNumber<-phenoInfo phenoInfo<-plotCurve radiationInfo radiationInfo<-radiationTypes radiationTypes<-RadioSet RadioSig radSensitivitySig sampleInfo sampleInfo<-sampleNames sampleNames<-sensitivityInfo sensitivityInfo<-sensitivityMeasures sensitivityProfiles sensitivityProfiles<-sensitivityRaw sensitivityRaw<-sensNumber sensNumber<-show showSigAnnot subsetTo summarizeMolecularProfiles summarizeSensitivityProfiles treatmentInfo treatmentInfo<-treatmentNames treatmentNames<-treatmentResponse treatmentResponse<-updateObject

Dependencies:abind assertthat backports base64enc bench BH Biobase BiocBaseUtils BiocGenerics BiocParallel bitops bslib BumpyMatrix cachem caTools celestial checkmate cli cluster codetools commonmark CoreGx cowplot cpp11 crayon crosstalk data.table DelayedArray digest downloader dplyr DT evaluate farver fastmap fastmatch fgsea fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gplots gtable gtools highr htmltools htmlwidgets httpuv igraph IRanges isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lsa magicaxis magrittr mapproj maps marray MASS Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment NISTunits otel piano pillar pkgconfig plotrix plyr pracma profmem promises purrr R6 RANN rappdirs RColorBrewer Rcpp relations reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo sets shiny shinydashboard shinyjs slam sm snow SnowballC sourcetools SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun xtable XVector yaml

RadioGx: An R Package for Analysis of Large Radiogenomic Datasets

Rendered fromRadioGx.Rmdusingknitr::knitr

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

Help page	Topics
`[`	[,RadioSet,ANY,ANY,ANY-method
Return a table of RadioSets available for download	availableRSets
A function to verify the structure of a RadioSet	checkRSetStructure
Cleaveland_mut RadioSet subsetted	clevelandSmall
computeAUC: computes AUC	computeAUC
Compute D10	computeD10
Compute SF2	computeSF2
Get the dimensions of a RadioSet	dim,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 object	downloadRSet
Fit linear-quadratic curves to dose-response data	linearQuadraticModel
Plot radiation dose-response curve	plotCurve
RadioSet constructor	RadioSet
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 Constructor	RadioSig
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 RadioSet	show,RadioSet-method
Show RadioGx Signatures	show,RadioSig-method
Show the Annotations of a signature object	showSigAnnot,RadioSig-method
A function to subset a RadioSet to data containing only specified radiations, cells and genes	subsetTo,RadioSet-method
Takes molecular data from a RadioSet, and summarises them into one entry per drug	summarizeMolecularProfiles,RadioSet-method
Takes the sensitivity data from a RadioSet, and summarises them into a drug vs cell line table	summarizeSensitivityProfiles,RadioSet-method
Update the RadioSet class after changes in it struture or API	updateObject,RadioSet-method

Package: RadioGx 2.17.0

RadioGx: Analysis of Large-Scale Radio-Genomic Data

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