Package: GladiaTOX 1.23.0

PMP S.A. R Support

GladiaTOX: R Package for Processing High Content Screening data

GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.

Authors:Vincenzo Belcastro [aut, cre], Dayne L Filer [aut], Stephane Cano [aut]

GladiaTOX_1.23.0.tar.gz
GladiaTOX_1.23.0.zip(r-4.5)GladiaTOX_1.23.0.zip(r-4.4)GladiaTOX_1.23.0.zip(r-4.3)
GladiaTOX_1.23.0.tgz(r-4.4-any)GladiaTOX_1.23.0.tgz(r-4.3-any)
GladiaTOX_1.23.0.tar.gz(r-4.5-noble)GladiaTOX_1.23.0.tar.gz(r-4.4-noble)
GladiaTOX_1.23.0.tgz(r-4.4-emscripten)GladiaTOX_1.23.0.tgz(r-4.3-emscripten)
GladiaTOX.pdf |GladiaTOX.html✨
GladiaTOX/json (API)
NEWS

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

Peer review:

On BioConductor:GladiaTOX-1.23.0(bioc 3.21)GladiaTOX-1.22.0(bioc 3.20)

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

softwareworkflowstepnormalizationpreprocessingqualitycontrol

4.00 score 2 scripts 160 downloads 1 mentions 71 exports 59 dependencies

Last updated 23 days agofrom:c12ce38d1f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winNOTENov 18 2024
R-4.5-linuxNOTENov 18 2024
R-4.4-winNOTENov 18 2024
R-4.4-macNOTENov 18 2024
R-4.3-winNOTENov 18 2024
R-4.3-macNOTENov 18 2024

Exports:assignDefaultMthdsbuildAssayTabdeleteStudyexportResultForToxpiGUIexportResultTableglCheckInputglComputeToxIndglLoadInputglPlotPieglPlotPieLogoglPlotPosCtrlglPlotPosCtrlMECglPlotStatglPlotToxIndgtoxAddModelgtoxAICProbgtoxCalcVmadgtoxCode2CASNgtoxConfgtoxConfDefaultgtoxConfListgtoxConfLoadgtoxConfResetgtoxConfSavegtoxFitgtoxHillACXXgtoxHillConcgtoxHillValgtoxImportThermoDBgtoxListFldsgtoxLoadAcidgtoxLoadAeidgtoxLoadAidgtoxLoadApidgtoxLoadAsidgtoxLoadChemgtoxLoadClibgtoxLoadDatagtoxLoadVehiclegtoxLoadVmadgtoxLoadWaidgtoxMakeAeidPltsgtoxMthdAssigngtoxMthdCleargtoxMthdListgtoxMthdLoadgtoxObjCnstgtoxObjGnlsgtoxObjHillgtoxPlotErrBargtoxPlotFitcgtoxPlotFitsgtoxPlotM4IDgtoxPlotPiegtoxPlotPieLgndgtoxPlotPlategtoxPlotWingtoxPrepOtptgtoxQuerygtoxRegistergtoxReportgtoxRungtoxSendQuerygtoxSetWllqgtoxSubsetChidgtoxUpdategtoxWriteDataloadAnnotlulwprepareDatForDB

Dependencies:bitbit64bitopsblobbrewcachemclicolorspacecpp11data.tableDBIdplyrfansifarverfastmapgenericsggplot2ggrepelgluegtablehmsisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmunsellnlmenumDerivpillarpkgconfigplogrpurrrR6RColorBrewerRcppRCurlRJSONIOrlangRMariaDBRSQLitescalesstringistringrtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrXMLxtable

GladiaTOX: R Package for Processing High Content Screening data

Vincenzo Belcastro, Stephane Cano, Florian Martin

Rendered fromGladiaTOX.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-09-15
Started: 2019-04-11

Readme and manuals

Help Manual

Help pageTopics
Assign default processing methodsassignDefaultMthds
Prepare assay table mapping infobuildAssayTab
Functions for configuring the gtox packageConfigure functions gtoxConf gtoxConfDefault gtoxConfList gtoxConfLoad gtoxConfReset gtoxConfSave
Completely remove all data for a studydeleteStudy
Create the result table for the asi in inputexportResultForToxpiGUI
Create the result table for the asi in inputexportResultTable
Check validity of input fileglCheckInput
Create toxicological indicator values for all chemicals in inputglComputeToxInd
Check validity of input fileglLoadInput
Pie chart for Minimal Effective Concentrations (MEC) and AC50 plotglPlotPie
plot package logoglPlotPieLogo
Box plot for positive control checkglPlotPosCtrl
Box plot for positive control checkglPlotPosCtrlMEC
Box plot for Minimal Effective Concentrations (MEC) and AC50 plotglPlotStat
Plot toxicological indicator values for all chemicals in inputglPlotToxInd
Draw a gtox Model onto an exisiting plotgtoxAddModel
Calculate the AIC probabilitiesgtoxAICProb
Calculate and update the assay endpoint cutoff valuesgtoxCalcVmad
Convert chemical code to CAS Registry NumbergtoxCode2CASN
Fit the data with the constant, hill, and gain-loss modelsgtoxFit
Functions to solve the Hill modelgtoxHillACXX gtoxHillConc gtoxHillVal Hill model utilites
Import data from ThermoDB by study IDgtoxImportThermoDB
Load the field names for a tablegtoxListFlds
Load assay plate informationgtoxLoadApid
Load sample/chemical informationgtoxLoadChem
Load chemical library informationgtoxLoadClib
Load gtox datagtoxLoadData
Load vehicle informationgtoxLoadVehicle
Load cutoff values for assay endpointsgtoxLoadVmad
Load well annotation informationgtoxLoadWaid
Create a .pdf with dose-response plotsgtoxMakeAeidPlts
Functions for managing processing methodsgtoxMthdAssign gtoxMthdClear gtoxMthdList gtoxMthdLoad Method functions
Create error bar plotsgtoxPlotErrBar
Plot the fit category treegtoxPlotFitc
Plot summary fits based on fit and dose-response datagtoxPlotFits
Plot fit summary plot by m4idgtoxPlotM4ID
Create piechart plotsgtoxPlotPie
Create piechart plot legendgtoxPlotPieLgnd
Plot plate heatmapgtoxPlotPlate
Create winning curve plotsgtoxPlotWin
Map assay/chemcial ID values to annotation informationgtoxPrepOtpt
Wrappers for sending queries and fetching resultsgtoxQuery gtoxSendQuery Query functions
Functions for registering & updating annotation informationgtoxRegister gtoxUpdate Register/update annotation
Generate a reportgtoxReport
Perform data processinggtoxRun
Change the well quality for a vector of lvl 0 IDsgtoxSetWllq
Subset level 5 data to a single sample per chemicalgtoxSubsetChid
Write screening data into the gtox databasesgtoxWriteData
Functions for loading assay informationgtoxLoadAcid gtoxLoadAeid gtoxLoadAid gtoxLoadAsid Load assay information
Register the annotations provided by GUIloadAnnot
Abbreviation for 'length(unique(x))'lu
Abbreviation for 'length(which(x))'lw
Model objective functionsgtoxObjCnst gtoxObjGnls gtoxObjHill Models
Assign default processing methodsprepareDatForDB