Package: ToxicoGx 2.9.0
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:
ToxicoGx_2.9.0.tar.gz
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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')) |
- HCC_sig - HCC_sig dataset
- TGGATESsmall - TGGATESsmall dataset
On BioConductor:ToxicoGx-2.9.0(bioc 3.20)ToxicoGx-2.8.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:bff4f5febc
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| '[' | [,ToxicoSet,ANY,ANY,ANY-method |
| Return a table of ToxicoSets available for download | availableTSets |
| A function to verify the structure of a ToxicoSet | checkTSetStructure |
| Computes the AUC for a Drug Dose Viability Curve | computeAUC |
| Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve | computeIC50 computeICn |
| Generic method for performing differential expression analysis on an S4 object using the limma package | computeLimmaDiffExpr |
| Conduct differential expression analysis using the limma R pacakge | computeLimmaDiffExpr,ToxicoSet-method |
| Get the dimensions of a ToxicoSet | dim,ToxicoSet-method |
| Download a ToxicoSet object | downloadTSet |
| Compares gene expression for a specificed set of features over specific drug dosages vs time | drugGeneResponseCurve |
| Drug perturbation analysis | drugPerturbationSig |
| Compares viabilities at a given dose over different experimental durations | drugTimeResponseCurve |
| HCC_sig dataset | HCC_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 ToxicoSet | show,ToxicoSet-method |
| Show ToxicoGx Signatures | show,ToxicoSig-method |
| Show the Annotations of a signature object | showSigAnnot |
| A function to subset a ToxicoSet to data containing only specified drugs, cells and genes | subsetTo |
| 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 table | summarizeSensitivityProfiles |
| TGGATESsmall dataset | TGGATESsmall |
| ToxicoSet constructor | ToxicoSet |
| 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 API | updateObject,ToxicoSet-method |
