Package: ToxicoGx 2.11.0

Benjamin Haibe-Kains

ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

Authors:Sisira Nair [aut], Esther Yoo [aut], Christopher Eeles [aut], Amy Tang [aut], Nehme El-Hachem [aut], Petr Smirnov [aut], Jermiah Joseph [aut], Benjamin Haibe-Kains [aut, cre]

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ToxicoGx.pdf |ToxicoGx.html✨
ToxicoGx/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:ToxicoGx-2.11.0(bioc 3.21)ToxicoGx-2.10.0(bioc 3.20)

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

geneexpressionpharmacogeneticspharmacogenomicssoftware

4.36 score 23 scripts 194 downloads 68 exports 135 dependencies

Last updated 2 months agofrom:15ee7e70b2. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:.convertTsetMolecularProfilesToSEannotationannotation<-availableTSetscheckTSetStructurecomputeAUCcomputeIC50computeICncomputeLimmaDiffExprcurationcuration<-datasetTypedatasetType<-dateCreateddateCreated<-downloadTSetdrugGeneResponseCurvedrugInfodrugInfo<-drugNamesdrugNames<-drugPerturbationSigdrugTimeResponseCurvefeatureInfofeatureInfo<-fNamesfNames<-geneDrugPerturbationlogLogisticRegressionmDataNamesmDataNames<-molecularProfilesmolecularProfiles<-molecularProfilesSlotmolecularProfilesSlot<-namename<-pertNumberpertNumber<-phenoInfophenoInfo<-sampleInfosampleInfo<-sampleNamessampleNames<-sensitivityInfosensitivityInfo<-sensitivityMeasuressensitivityProfilessensitivityProfiles<-sensitivityRawsensitivityRaw<-sensNumbersensNumber<-showshowSigAnnotsubsetTosummarizeMolecularProfilessummarizeSensitivityProfilesToxicoSetToxicoSigtreatmentInfotreatmentInfo<-treatmentNamestreatmentNames<-treatmentResponsetreatmentResponse<-updateObject

Dependencies:abindaskpassassertthatbackportsbase64encbenchBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbitopsbslibBumpyMatrixcachemcaToolscheckmatecliclustercodetoolscolorspacecommonmarkCoreGxcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdownloaderdplyrDTevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalsamagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmeopensslpianopillarpkgconfigplyrprofmempromisespurrrR6rappdirsRColorBrewerRcpprelationsreshape2rlangrmarkdownS4ArraysS4VectorssassscalessetsshinyshinydashboardshinyjsslamsnowSnowballCsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevisNetworkwithrxfunxtableXVectoryamlzlibbioc

ToxicoGx: An R Platform for Integrated Toxicogenomics Data Analysis

Sisira Kadambat Nair, Esther Yoo, Christopher Eeles, Amy Tang, Nehme El-Hachem, Petr Smirnov, Benjamin Haibe-Kains

Rendered fromtoxicoGxCaseStudies.Rmdusingknitr::knitron Dec 18 2024.

Last update: 2022-04-22
Started: 2019-10-15

Readme and manuals

Help Manual

Help pageTopics
'['[,ToxicoSet,ANY,ANY,ANY-method
Return a table of ToxicoSets available for downloadavailableTSets
A function to verify the structure of a ToxicoSetcheckTSetStructure
Computes the AUC for a Drug Dose Viability CurvecomputeAUC
Computes the ICn for any n in 0-100 for a Drug Dose Viability CurvecomputeIC50 computeICn
Generic method for performing differential expression analysis on an S4 object using the limma packagecomputeLimmaDiffExpr
Conduct differential expression analysis using the limma R pacakgecomputeLimmaDiffExpr,ToxicoSet-method
Get the dimensions of a ToxicoSetdim,ToxicoSet-method
Download a ToxicoSet objectdownloadTSet
Compares gene expression for a specificed set of features over specific drug dosages vs timedrugGeneResponseCurve
Drug perturbation analysisdrugPerturbationSig
Compares viabilities at a given dose over different experimental durationsdrugTimeResponseCurve
HCC_sig datasetHCC_sig
Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.logLogisticRegression
Show a ToxicoSetshow,ToxicoSet-method
Show ToxicoGx Signaturesshow,ToxicoSig-method
Show the Annotations of a signature objectshowSigAnnot
A function to subset a ToxicoSet to data containing only specified drugs, cells and genessubsetTo
Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.summarizeMolecularProfiles
Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line tablesummarizeSensitivityProfiles
TGGATESsmall datasetTGGATESsmall
ToxicoSet constructorToxicoSet
Accessing and modifying information in a 'CoreSet'annotation annotation,ToxicoSet-method annotation<- annotation<-,ToxicoSet,list-method cellInfo cellInfo,ToxicoSet-method cellInfo<- cellInfo<-,ToxicoSet,data.frame-method cellName,ToxicoSet-method cellNames cellNames<- cellNames<-,ToxicoSet,list-method curation curation,ToxicoSet-method curation<- curation<-,ToxicoSet,list-method datasetType datasetType,ToxicoSet-method datasetType<- datasetType<-,ToxicoSet,character-method dateCreated dateCreated,ToxicoSet-method dateCreated<- dateCreated<-,ToxicoSet,character-method dateCreated<-,ToxicoSet-method drugInfo drugInfo<- drugNames drugNames<- featureInfo featureInfo,ToxicoSet-method featureInfo<- featureInfo<-,ToxicoSet,character,data.frame-method featureInfo<-,ToxicoSet,character,DataFrame-method fNames fNames,ToxicoSet,character-method fNames<- fNames<-,ToxicoSet,character,character-method mDataNames mDataNames,ToxicoSet-method mDataNames<- mDataNames<-,ToxicoSet,ANY-method mDataNames<-,ToxicoSet-method molecularProfiles molecularProfiles,ToxicoSet-method molecularProfiles<- molecularProfiles<-,ToxicoSet,character,character,matrix-method molecularProfiles<-,ToxicoSet,character,missing,matrix-method molecularProfiles<-,ToxicoSet,missing,missing,list-method molecularProfiles<-,ToxicoSet,missing,missing,MutliAssayExperiment-method molecularProfilesSlot molecularProfilesSlot,ToxicoSet-method molecularProfilesSlot<- molecularProfilesSlot<-,ToxicoSet,list-method molecularProfilesSlot<-,ToxicoSet,list_OR_MAE-method molecularProfilesSlot<-ToxicoSet,MultiAssayExperiment-method moleculerProfilesSlot,ToxicoSet-method name name,ToxicoSet-method name<- name<-,ToxicoSet,character-method name<-,ToxicoSet-method pertNumber pertNumber,ToxicoSet-method pertNumber<- pertNumber<-,ToxicoSet,array-method phenoInfo phenoInfo,ToxicoSet,character-method phenoInfo<- phenoInfo<-,ToxicoSet,character,data.frame-method phenoInfo<-,ToxicoSet,character,DataFrame-method sampleInfo sampleInfo,ToxicoSet-method sampleInfo<- sampleInfo<-,ToxicoSet,data.frame-method sampleName,ToxicoSet-method sampleNames sampleNames,ToxicoSet-method sampleNames<- sampleNames<-,ToxicoSet,character-method sampleNames<-,ToxicoSet,list-method sensitivityInfo,ToxicoSet,character-method sensitivityInfo,ToxicoSet,missing-method sensitivityInfo,ToxicoSet-method sensitivityInfo<-,ToxicoSet,data.frame-method sensitivityInfo<-,ToxicoSet,missing,data.frame-method sensitivityMeasures,ToxicoSet-method sensitivityMeasures<-,ToxicoSet,character-method sensitivityProfiles,ToxicoSet-method sensitivityProfiles<-,ToxicoSet,data.frame-method sensitivityRaw,ToxicoSet-method sensitivityRaw<-,ToxicoSet,array-method sensitivitySlot sensitivitySlot<- sensitvityInfo<-,ToxicoSet,character,data.frame-method sensNumber sensNumber,ToxicoSet-method sensNumber<- sensNumber<-,ToxicoSet,matrix-method ToxicoSet-accessors treamentResponse<-,ToxicoSet,list-method treatmentInfo treatmentInfo,ToxicoSet-method treatmentInfo<- treatmentInfo<-,ToxicoSet,data.frame-method treatmentNames treatmentNames,ToxicoSet-method treatmentNames<- treatmentNames<-,ToxicoSet,character-method treatmentResponse treatmentResponse,ToxicoSet-method treatmentResponse<- treatmentResponse<-,ToxicoSet,list_OR_LongTable-method treatmentResponse<-,ToxicoSet,LongTable-method
Class to contain Toxico-genomic Data.ToxicoSet ToxicoSet-class
Update the ToxicoSet class after changes in it struture or APIupdateObject,ToxicoSet-method