Package: GladiaTOX 1.29.0

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_1.29.0.tar.gz
GladiaTOX_1.29.0.zip(r-4.7)GladiaTOX_1.29.0.zip(r-4.6)GladiaTOX_1.29.0.zip(r-4.5)
GladiaTOX_1.29.0.tgz(r-4.6-any)GladiaTOX_1.29.0.tgz(r-4.5-any)
GladiaTOX_1.29.0.tar.gz(r-4.7-any)GladiaTOX_1.29.0.tar.gz(r-4.6-any)
GladiaTOX_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GladiaTOX/json (API)

# Install 'GladiaTOX' in R:

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

Bug tracker:https://github.com/philipmorrisintl/gladiatox/issues

On BioConductor:GladiaTOX-1.29.0(bioc 3.24)GladiaTOX-1.28.0(bioc 3.23)

software workflowstep normalization preprocessing qualitycontrol

5.08 score 2 scripts 1 mentions 71 exports 51 dependencies

Last updated from:ea22155c78. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	219
linux-devel-x86_64	NOTE	230
source / vignettes	OK	390
linux-release-x86_64	NOTE	291
macos-release-arm64	NOTE	187
macos-oldrel-arm64	NOTE	152
windows-devel	NOTE	201
windows-release	NOTE	190
windows-oldrel	NOTE	354
wasm-release	OK	153

Exports:assignDefaultMthds buildAssayTab deleteStudy exportResultForToxpiGUI exportResultTable glCheckInput glComputeToxInd glLoadInput glPlotPie glPlotPieLogo glPlotPosCtrl glPlotPosCtrlMEC glPlotStat glPlotToxInd gtoxAddModel gtoxAICProb gtoxCalcVmad gtoxCode2CASN gtoxConf gtoxConfDefault gtoxConfList gtoxConfLoad gtoxConfReset gtoxConfSave gtoxFit gtoxHillACXX gtoxHillConc gtoxHillVal gtoxImportThermoDB gtoxListFlds gtoxLoadAcid gtoxLoadAeid gtoxLoadAid gtoxLoadApid gtoxLoadAsid gtoxLoadChem gtoxLoadClib gtoxLoadData gtoxLoadVehicle gtoxLoadVmad gtoxLoadWaid gtoxMakeAeidPlts gtoxMthdAssign gtoxMthdClear gtoxMthdList gtoxMthdLoad gtoxObjCnst gtoxObjGnls gtoxObjHill gtoxPlotErrBar gtoxPlotFitc gtoxPlotFits gtoxPlotM4ID gtoxPlotPie gtoxPlotPieLgnd gtoxPlotPlate gtoxPlotWin gtoxPrepOtpt gtoxQuery gtoxRegister gtoxReport gtoxRun gtoxSendQuery gtoxSetWllq gtoxSubsetChid gtoxUpdate gtoxWriteData loadAnnot lu lw prepareDatForDB

Dependencies:bit bit64 bitops blob brew cachem cli cpp11 data.table DBI dplyr farver fastmap generics ggplot2 ggrepel glue gtable hms isoband labeling lifecycle lubridate magrittr memoise numDeriv pillar pkgconfig purrr R6 RColorBrewer Rcpp RCurl RJSONIO rlang RMariaDB RSQLite S7 scales stringi stringr tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr XML xtable

GladiaTOX: R Package for Processing High Content Screening data

Rendered fromGladiaTOX.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign default processing methods	assignDefaultMthds
Prepare assay table mapping info	buildAssayTab
Functions for configuring the gtox package	Configure functions gtoxConf gtoxConfDefault gtoxConfList gtoxConfLoad gtoxConfReset gtoxConfSave
Completely remove all data for a study	deleteStudy
Create the result table for the asi in input	exportResultForToxpiGUI
Create the result table for the asi in input	exportResultTable
Check validity of input file	glCheckInput
Create toxicological indicator values for all chemicals in input	glComputeToxInd
Check validity of input file	glLoadInput
Pie chart for Minimal Effective Concentrations (MEC) and AC50 plot	glPlotPie
plot package logo	glPlotPieLogo
Box plot for positive control check	glPlotPosCtrl
Box plot for positive control check	glPlotPosCtrlMEC
Box plot for Minimal Effective Concentrations (MEC) and AC50 plot	glPlotStat
Plot toxicological indicator values for all chemicals in input	glPlotToxInd
Draw a gtox Model onto an exisiting plot	gtoxAddModel
Calculate the AIC probabilities	gtoxAICProb
Calculate and update the assay endpoint cutoff values	gtoxCalcVmad
Convert chemical code to CAS Registry Number	gtoxCode2CASN
Fit the data with the constant, hill, and gain-loss models	gtoxFit
Functions to solve the Hill model	gtoxHillACXX gtoxHillConc gtoxHillVal Hill model utilites
Import data from ThermoDB by study ID	gtoxImportThermoDB
Load the field names for a table	gtoxListFlds
Load assay plate information	gtoxLoadApid
Load sample/chemical information	gtoxLoadChem
Load chemical library information	gtoxLoadClib
Load gtox data	gtoxLoadData
Load vehicle information	gtoxLoadVehicle
Load cutoff values for assay endpoints	gtoxLoadVmad
Load well annotation information	gtoxLoadWaid
Create a .pdf with dose-response plots	gtoxMakeAeidPlts
Functions for managing processing methods	gtoxMthdAssign gtoxMthdClear gtoxMthdList gtoxMthdLoad Method functions
Create error bar plots	gtoxPlotErrBar
Plot the fit category tree	gtoxPlotFitc
Plot summary fits based on fit and dose-response data	gtoxPlotFits
Plot fit summary plot by m4id	gtoxPlotM4ID
Create piechart plots	gtoxPlotPie
Create piechart plot legend	gtoxPlotPieLgnd
Plot plate heatmap	gtoxPlotPlate
Create winning curve plots	gtoxPlotWin
Map assay/chemcial ID values to annotation information	gtoxPrepOtpt
Wrappers for sending queries and fetching results	gtoxQuery gtoxSendQuery Query functions
Functions for registering & updating annotation information	gtoxRegister gtoxUpdate Register/update annotation
Generate a report	gtoxReport
Perform data processing	gtoxRun
Change the well quality for a vector of lvl 0 IDs	gtoxSetWllq
Subset level 5 data to a single sample per chemical	gtoxSubsetChid
Write screening data into the gtox databases	gtoxWriteData
Functions for loading assay information	gtoxLoadAcid gtoxLoadAeid gtoxLoadAid gtoxLoadAsid Load assay information
Register the annotations provided by GUI	loadAnnot
Abbreviation for 'length(unique(x))'	lu
Abbreviation for 'length(which(x))'	lw
Model objective functions	gtoxObjCnst gtoxObjGnls gtoxObjHill Models
Assign default processing methods	prepareDatForDB

Package: GladiaTOX 1.29.0

GladiaTOX: R Package for Processing High Content Screening data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)