Package: ToxicoGx 2.17.0

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]

ToxicoGx_2.17.0.tar.gz
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ToxicoGx_2.17.0.tgz(r-4.6-any)ToxicoGx_2.17.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ToxicoGx/json (API)

# Install 'ToxicoGx' in R:

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

Datasets:

HCC_sig - HCC_sig dataset
TGGATESsmall - TGGATESsmall dataset

On BioConductor:ToxicoGx-2.17.0(bioc 3.24)ToxicoGx-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.

geneexpression pharmacogenetics pharmacogenomics software

4.40 score 25 scripts 68 exports 123 dependencies

Last updated from:8cb09beab4. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	227
linux-devel-x86_64	NOTE	386
source / vignettes	OK	347
linux-release-x86_64	NOTE	417
macos-release-arm64	NOTE	228
macos-oldrel-arm64	NOTE	187
windows-devel	NOTE	329
windows-release	NOTE	291
windows-oldrel	NOTE	285
wasm-release	OK	216

Exports:.convertTsetMolecularProfilesToSE annotation annotation<-availableTSets checkTSetStructure computeAUC computeIC50 computeICn computeLimmaDiffExpr curation curation<-datasetType datasetType<-dateCreated dateCreated<-downloadTSet drugGeneResponseCurve drugInfo drugInfo<-drugNames drugNames<-drugPerturbationSig drugTimeResponseCurve featureInfo featureInfo<-fNames fNames<-geneDrugPerturbation logLogisticRegression mDataNames mDataNames<-molecularProfiles molecularProfiles<-molecularProfilesSlot molecularProfilesSlot<-name name<-pertNumber pertNumber<-phenoInfo phenoInfo<-sampleInfo sampleInfo<-sampleNames sampleNames<-sensitivityInfo sensitivityInfo<-sensitivityMeasures sensitivityProfiles sensitivityProfiles<-sensitivityRaw sensitivityRaw<-sensNumber sensNumber<-show showSigAnnot subsetTo summarizeMolecularProfiles summarizeSensitivityProfiles ToxicoSet ToxicoSig treatmentInfo treatmentInfo<-treatmentNames treatmentNames<-treatmentResponse treatmentResponse<-updateObject

Dependencies:abind assertthat backports base64enc bench BH Biobase BiocBaseUtils BiocGenerics BiocParallel bitops bslib BumpyMatrix cachem caTools 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 magrittr marray Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment otel piano pillar pkgconfig plyr profmem promises purrr R6 rappdirs RColorBrewer Rcpp relations reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo sets shiny shinydashboard shinyjs slam snow SnowballC sourcetools SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun xtable XVector yaml

ToxicoGx: An R Platform for Integrated Toxicogenomics Data Analysis

Plotting gene expression changes from TG-GATEs dataset | Connectivity map analysis on TG-GATEs and human hepatocarcinoma signatures

Rendered fromtoxicoGxCaseStudies.Rmdusingknitr::knitr

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

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

Package: ToxicoGx 2.17.0

ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

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