cellHTS2: Analysis of cell-based screens - revised version of cellHTS
Version 2.40.0

This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.

AuthorLigia Bras, Wolfgang Huber <whuber@embl.de>, Michael Boutros <m.boutros@dkfz.de>, Gregoire Pau <gpau@embl.de>, Florian Hahne <florian.hahne@novartis.com>
Bioconductor views CellBasedAssays Preprocessing Visualization
Date of publicationNone
MaintainerJoseph Barry <joseph.barry@embl.de>
LicenseArtistic-2.0
Version2.40.0
URL http://www.dkfz.de/signaling http://www.ebi.ac.uk/huber
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cellHTS2")

Popular man pages

batch: Access and replace the batch information of a cellHTS object
bdgpbiomart: Dataset with annotation of CG identifiers
getZfactor: Per-experiment Z'-factor of a cellHTS object
readPlateList: Read a collection of plate reader data files
ROC: Creates an object of class "ROC" which can be plotted as a...
rsa: Perform RSA ranking on the screening results.
summarizeChannels: Summarization of dual-channel data
See all...

All man pages Function index File listing

Man pages

annotate: Annotates the reagents (probes) of a cellHTS object
batch: Access and replace the batch information of a cellHTS object
bdgpbiomart: Dataset with annotation of CG identifiers
Bscore: B score normalization
buildCellHTS2: Build a cellHTS2 object from a data frame containing...
cellHTS2: cellHTS2 Package Overview
cellHTS-class: A class for data from cell-based high-throughput assays...
configurationAsScreenPlot: Screen plot of the plate configuration of a cellHTS object
configure: Configures the plates and plate result files
convertOldCellHTS: Convert an old S3 class cellHTS object to the new S4 class...
convertWellCoordinates: Converts different well identifiers
Data: Access and replace the assayData slot of a cellHTS object
data-dualCh: A sample cellHTS object containing dual channel data
data-KcViab: A sample cellHTS object - D. melanogaster genome-wide RNAi...
data-KcViabSmall: A sample cellHTS object - D. melanogaster genome-wide RNAi...
data-oldKcViabSmall: A sample S3 class cellHTS object - D. melanogaster...
getDynamicRange: Per-plate dynamic range of a cellHTS object
getEnVisionRawData: Read a plate file obtain from EnVision Plate Reader
getMeasureRepAgreement: Measures of agreement between plate replicates from a cellHTS...
getTopTable: Generate the hit list from a scored cellHTS object
getZfactor: Per-experiment Z'-factor of a cellHTS object
gseaModule: Constructor for an object of class gseaModule
imageScreen: Experiment-wide quality control plot of a cellHTS object
intensityFiles: Retrieve the contents of the input files used to generate a...
normalizePlates: Per-plate data transformation, normalization and variance...
oneRowPerId: Rearrange dataframe entries such that there is exactly one...
plate: Retrieve information related with the format of a RNAi...
plateEffects: Access plate effects stored in a cellHTS object.
plotSpatialEffects: Plate plot with the row and column offsets estimated by the a...
readHTAnalystData: Read a set of plate results obtained from a HTanalyser plate...
readPlateList: Read a collection of plate reader data files
ROC: Creates an object of class "ROC" which can be plotted as a...
ROC-class: Class that contain data that can be plotted as a ROC curve.
rsa: Perform RSA ranking on the screening results.
scoreReplicates: Scores normalized replicate values given in a cellHTS object
scores2calls: Sigmoidal transformation of the score values stored in a...
setSettings: cellHTS2 HTML report settings
spatialNormalization: Spatial normalization
state: Retrieve the state of a cellHTS object.
summarizeChannels: Summarization of dual-channel data
summarizeReplicates: Summarize between scored replicate values given in a cellHTS...
templateDescriptionFile: Creates a template description file for an RNAi experiment
updateCellHTS: Update old serialized cellHTS objects.
wellAnno: Access the annotation from a cellHTS object.
writeReport: Create a directory with HTML pages of linked tables and plots...
writeTab: Write the data from a cellHTS object to a tab-delimited file
write.tabdel: Wrapper to function 'write.table' used to write data to a...

Functions

Bscore Man page Source code
Data Man page
Data,cellHTS-method Man page
Data<- Man page
Data<-,cellHTS,array-method Man page
KcViab Man page
KcViabSmall Man page
NPI Source code
OPI Source code
OPIScore Source code
POC Source code
QMbyPlate Source code
QMexperiment Source code
ROC Man page
ROC,cellHTS-method Man page
ROC-class Man page
addTooltip Source code
adjustVariance Source code
adjustVariancebyBatch Source code
adjustVariancebyExperiment Source code
adjustVariancebyPlate Source code
annotate Man page
annotate,cellHTS-method Man page
barplotWithImageMap Source code
batch Man page
batch,cellHTS-method Man page
batch<- Man page
batch<-,cellHTS,data.frame-method Man page
bdgpbiomart Man page
boxplotwithNA Source code
buildCellHTS2 Man page Source code
cellHTS Man page
cellHTS-class Man page
cellHTS2 Man page
cellHTS2-package Man page
cellHTSlistVerification Source code
chanCorrFun Source code
checkClass Source code
checkColumns Source code
checkControls Source code
checkControls2W Source code
checkMandatoryColumns Source code
checkPosControls Source code
chtsGetSetting Source code
chtsImage Source code
chtsImageStack Source code
chtsModule Source code
chtsSetSetting Source code
class.cellHTS Man page
coerce,chtsImage,data.frame-method Man page
colors4Controls Source code
compare2cellHTS Man page
compare2cellHTS,cellHTS,cellHTS-method Man page
configurationAsScreenPlot Man page Source code
configure Man page
configure,cellHTS-method Man page
controlsBasedNormalization Source code
controlsplot Source code
convertOldCellHTS Man page Source code
convertWellCoordinates Man page Source code
corrFun Source code
createOutputFolder Source code
createProgressList Source code
ctrlsPerPlate Source code
dataframeOutput Source code
densityplot Source code
dualCh Man page
dynRange Source code
emptyOrNA Source code
envisionPlateReader Source code
equalOrZero Source code
evalGseaModule Source code
extractTag Source code
findControls Source code
funOperator Source code
geneAnno Man page
geneAnno,cellHTS-method Man page
getArrayCorrectWellAnno Source code
getConfiguration Source code
getControlsPositions Source code
getDefinition Source code
getDynamicRange Man page Source code
getEnVisionCrosstalkCorrectedData Man page Source code
getEnVisionRawData Man page Source code
getMeasureRepAgreement Man page Source code
getNrPlateColRow Source code
getPlist Source code
getProInfo Source code
getScreendesc Source code
getScreenlog Source code
getSettings Man page Source code
getTopTable Man page Source code
getZfactor Man page Source code
gseaModule Man page Source code
guid Source code
handleOneGroup Source code
histFun Source code
imageScreen Man page Source code
imageScreenArgsVerification Source code
initialize,cellHTS-method Man page
intensFun Source code
intensityFiles Man page
intensityFiles,cellHTS-method Man page
isUpToDate Source code
length,GeneSet-method Man page
lines,ROC-method Man page Man page
maFun Source code
makePlot Source code
meanSdPlot Man page
meanSdPlot,cellHTS-method Man page
myApplyByCategory Source code
myCall Source code
myImageMap Source code
myUpdateProgress Source code
name Man page
name,cellHTS-method Man page
name<- Man page
name<-,cellHTS,character-method Man page
nbatch Man page
nbatch,cellHTS-method Man page
normalizePlates Man page Source code
oldKcViabSmall Man page
onAttach Source code
onLoad Source code
oneRowPerId Man page Source code
optimalDevDims Source code
parseGlossaryXML Source code
parseLetNum Source code
pdim Man page
pdim,cellHTS-method Man page Man page
perCatPage Source code
perPlateScaling Source code
plate Man page
plate,cellHTS-method Man page
plateConf Man page
plateConf,cellHTS-method Man page
plateEffects Man page
plateEffects,cellHTS-method Man page
plateList Man page
plateList,cellHTS-method Man page
plateListClass Source code
plot,ROC,missing-method Man page Man page
plot,ROC-method Man page Man page
plotPlateArgsVerification Source code
plotSpatialEffects Man page Source code
position Man page
position,cellHTS-method Man page
readHTAnalystData Man page Source code
readHTAnalystOneReplicate Source code
readPlateList Man page Source code
rsa Man page Source code
saveHtmlGlossary Source code
scoreReplicates Man page Source code
scoreReplicatesByNPI Source code
scoreReplicatesByzscore Source code
scores2calls Man page Source code
screenDesc Man page
screenDesc,cellHTS-method Man page
screenImageMap Source code
screenLog Man page
screenLog,cellHTS-method Man page
sdFun Source code
setDefinition Source code
setSettings Man page Source code
settings Man page
show,ROC-method Man page
show,cellHTS-method Man page
spatialNormalization Man page Source code
standardizeWellID Source code
state Man page
state,cellHTS-method Man page
summarizeChannels Man page Source code
summarizeReplicates Man page Source code
tableOutput Source code
tableOutputWithHeaderRows Source code
templateDescriptionFile Man page Source code
updateCellHTS Man page Source code
validityCellHTS Source code
validityROC Source code
well Man page
well,cellHTS-method Man page
wellAnno Man page
wellAnno,cellHTS-method Man page
write.tabdel Man page Source code
writeHtml.experimentQC Source code
writeHtml.gseaModule Source code
writeHtml.header Source code
writeHtml.mainpage Source code
writeHtml.plateConf Source code
writeHtml.plateList Source code
writeHtml.screenDescription Source code
writeHtml.screenResults Source code
writeHtml.screenScript Source code
writeHtml.screenSummary Source code
writeHtml.tab Source code
writeHtml.tabCollection Source code
writeHtml.trailer Source code
writeImgRef Source code
writeIntensityFiles Source code
writeQCTable Source code
writeReport Man page Source code
writeTab Man page
writeTab,cellHTS-method Man page
zfacFun Source code

Files

.Rinstignore
CHANGES
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/adjustVariance.R
R/checkColumns.R
R/checkControls.R
R/convertOldCellHTS.R
R/envisionPlateReader.R
R/getDynamicRange.R
R/getMeasureRepAgreement.R
R/getTopTable.R
R/getZfactor.R
R/glossary.R
R/gseaModule.R
R/htmlFunctions.R
R/imageScreen.R
R/makePlot.R
R/methods-ROC.R
R/methods-cellHTS.R
R/normalizePlates.R
R/oneRowPerId.R
R/perPlateScaling.R
R/plateConfModule.R
R/plateListModule.R
R/plateSummariesModule.R
R/plotSpatialEffects.R
R/progressReport.R
R/readHTAnalystData.R
R/readPlateList.R
R/rsa.R
R/screenDescriptionModule.R
R/screenResultsModule.R
R/screenScriptModule.R
R/screenSummaryModule.R
R/settings.R
R/summarizeReplicates.R
R/tableOutput.R
R/templateDescriptionFile.R
R/write.tabdel.R
R/writeHTML-methods.R
R/writeReport.R
R/zzz.R
build
build/vignette.rds
data
data/KcViab.rda
data/KcViabSmall.rda
data/bdgpbiomart.rda
data/dualCh.rda
data/oldKcViabSmall.rda
inst
inst/CITATION
inst/DualChannelScreen
inst/DualChannelScreen/Description.txt
inst/DualChannelScreen/Plateconf.txt
inst/DualChannelScreen/Platelist.txt
inst/DualChannelScreen/RA01D1.TXT
inst/DualChannelScreen/RA01D2.TXT
inst/DualChannelScreen/RA02D1.TXT
inst/DualChannelScreen/RA02D2.TXT
inst/DualChannelScreen/RA03D1.TXT
inst/DualChannelScreen/RA03D2.TXT
inst/DualChannelScreen/RB01D1.TXT
inst/DualChannelScreen/RB01D2.TXT
inst/DualChannelScreen/RB02D1.TXT
inst/DualChannelScreen/RB02D2.TXT
inst/DualChannelScreen/RB03D1.TXT
inst/DualChannelScreen/RB03D2.TXT
inst/DualChannelScreen/Screenlog.txt
inst/EnVisionExample
inst/EnVisionExample/XXX_1500.csv
inst/EnVisionExample/platelist.txt
inst/KcCellTiter
inst/KcCellTiter/Description.txt
inst/KcCellTiter/KcCellTiter0607.txt
inst/KcCellTiter/KcCellTiter0707.txt
inst/KcCellTiter/Plateconf.txt
inst/KcCellTiter/Screenlog.txt
inst/KcViab
inst/KcViab/Analysis2003.txt
inst/KcViab/Description.txt
inst/KcViab/FT01-G01.txt
inst/KcViab/FT01-G02.txt
inst/KcViab/FT02-G01.txt
inst/KcViab/FT02-G02.txt
inst/KcViab/FT03-G01.txt
inst/KcViab/FT03-G02.txt
inst/KcViab/FT04-G01.txt
inst/KcViab/FT04-G02.txt
inst/KcViab/FT05-G01.txt
inst/KcViab/FT05-G02.txt
inst/KcViab/FT06-G01.txt
inst/KcViab/FT06-G02.txt
inst/KcViab/FT07-G01.txt
inst/KcViab/FT07-G02.txt
inst/KcViab/FT08-G01.txt
inst/KcViab/FT08-G02.txt
inst/KcViab/FT09-G01.txt
inst/KcViab/FT09-G02.txt
inst/KcViab/FT10-G01.txt
inst/KcViab/FT10-G02.txt
inst/KcViab/FT11-G01.txt
inst/KcViab/FT11-G02.txt
inst/KcViab/FT12-G01.txt
inst/KcViab/FT12-G02.txt
inst/KcViab/FT13-G01.txt
inst/KcViab/FT13-G02.txt
inst/KcViab/FT14-G01.txt
inst/KcViab/FT14-G02.txt
inst/KcViab/FT15-G01.txt
inst/KcViab/FT15-G02.txt
inst/KcViab/FT16-G01.txt
inst/KcViab/FT16-G02.txt
inst/KcViab/FT17-G01.txt
inst/KcViab/FT17-G02.txt
inst/KcViab/FT18-G01.txt
inst/KcViab/FT18-G02.txt
inst/KcViab/FT19-G01.txt
inst/KcViab/FT19-G02.txt
inst/KcViab/FT20-G01.txt
inst/KcViab/FT20-G02.txt
inst/KcViab/FT21-G01.txt
inst/KcViab/FT21-G02.txt
inst/KcViab/FT22-G01.txt
inst/KcViab/FT22-G02.txt
inst/KcViab/FT23-G01.txt
inst/KcViab/FT23-G02.txt
inst/KcViab/FT24-G01.txt
inst/KcViab/FT24-G02.txt
inst/KcViab/FT25-G01.txt
inst/KcViab/FT25-G02.txt
inst/KcViab/FT26-G01.txt
inst/KcViab/FT26-G02.txt
inst/KcViab/FT27-G01.txt
inst/KcViab/FT27-G02.txt
inst/KcViab/FT28-G01.txt
inst/KcViab/FT28-G02.txt
inst/KcViab/FT29-G01.txt
inst/KcViab/FT29-G02.txt
inst/KcViab/FT30-G01.txt
inst/KcViab/FT30-G02.txt
inst/KcViab/FT31-G01.txt
inst/KcViab/FT31-G02.txt
inst/KcViab/FT32-G01.txt
inst/KcViab/FT32-G02.txt
inst/KcViab/FT33-G01.txt
inst/KcViab/FT33-G02.txt
inst/KcViab/FT34-G01.txt
inst/KcViab/FT34-G02.txt
inst/KcViab/FT35-G01.txt
inst/KcViab/FT35-G02.txt
inst/KcViab/FT36-G01.txt
inst/KcViab/FT36-G02.txt
inst/KcViab/FT37-G01.txt
inst/KcViab/FT37-G02.txt
inst/KcViab/FT38-G01.txt
inst/KcViab/FT38-G02.txt
inst/KcViab/FT39-G01.txt
inst/KcViab/FT39-G02.txt
inst/KcViab/FT40-G01.txt
inst/KcViab/FT40-G02.txt
inst/KcViab/FT41-G01.txt
inst/KcViab/FT41-G02.txt
inst/KcViab/FT42-G01.txt
inst/KcViab/FT42-G02.txt
inst/KcViab/FT43-G01.txt
inst/KcViab/FT43-G02.txt
inst/KcViab/FT44-G01.txt
inst/KcViab/FT44-G02.txt
inst/KcViab/FT45-G01.txt
inst/KcViab/FT45-G02.txt
inst/KcViab/FT46-G01.txt
inst/KcViab/FT46-G02.txt
inst/KcViab/FT47-G01.txt
inst/KcViab/FT47-G02.txt
inst/KcViab/FT48-G01.txt
inst/KcViab/FT48-G02.txt
inst/KcViab/FT49-G01.txt
inst/KcViab/FT49-G02.txt
inst/KcViab/FT50-G01.txt
inst/KcViab/FT50-G02.txt
inst/KcViab/FT51-G01.txt
inst/KcViab/FT51-G02.txt
inst/KcViab/FT52-G01.txt
inst/KcViab/FT52-G02.txt
inst/KcViab/FT53-G01.txt
inst/KcViab/FT53-G02.txt
inst/KcViab/FT54-G01.txt
inst/KcViab/FT54-G02.txt
inst/KcViab/FT55-G01.txt
inst/KcViab/FT55-G02.txt
inst/KcViab/FT56-G01.txt
inst/KcViab/FT56-G02.txt
inst/KcViab/FT57-G01.txt
inst/KcViab/FT57-G02.txt
inst/KcViab/GeneIDs_Dm_HFA_1.1.txt
inst/KcViab/Plateconf.txt
inst/KcViab/Platelist.txt
inst/KcViab/Screenlog.txt
inst/KcViab/old-Plateconf.txt
inst/KcViab/old-Screenlog.txt
inst/KcViabSmall
inst/KcViabSmall/Description.txt
inst/KcViabSmall/FT01-G01.txt
inst/KcViabSmall/FT01-G02.txt
inst/KcViabSmall/FT02-G01.txt
inst/KcViabSmall/FT02-G02.txt
inst/KcViabSmall/FT03-G01.txt
inst/KcViabSmall/FT03-G02.txt
inst/KcViabSmall/GeneIDs_Dm_HFAsubset_1.1.txt
inst/KcViabSmall/Plateconf.txt
inst/KcViabSmall/Platelist.txt
inst/KcViabSmall/Screenlog.txt
inst/TwoWayAssay
inst/TwoWayAssay/DHA001LU1.CSV
inst/TwoWayAssay/DHA001LU2.CSV
inst/TwoWayAssay/Description.txt
inst/TwoWayAssay/GeneIDs.txt
inst/TwoWayAssay/Plateconf.txt
inst/TwoWayAssay/Platelist.txt
inst/TwoWayAssay/importData.R
inst/doc
inst/doc/cellhts2.R
inst/doc/cellhts2.Rnw
inst/doc/cellhts2.pdf
inst/doc/cellhts2Complete.R
inst/doc/cellhts2Complete.Rnw
inst/doc/cellhts2Complete.pdf
inst/doc/twoChannels.R
inst/doc/twoChannels.Rnw
inst/doc/twoChannels.pdf
inst/doc/twoWay.R
inst/doc/twoWay.Rnw
inst/doc/twoWay.pdf
inst/glossary
inst/glossary/glossary.xml
inst/scripts
inst/scripts/dummy.R
inst/scripts/makeDatasets.R
inst/scripts/parsePackage.R
inst/templates
inst/templates/back.gif
inst/templates/backblue.gif
inst/templates/backbluesmall.gif
inst/templates/bordercorner.gif
inst/templates/cellHTS.css
inst/templates/cellHTS.js
inst/templates/checkmark.png
inst/templates/failed.png
inst/templates/leftblue.gif
inst/templates/leftbluemid.gif
inst/templates/leftbluesmall.gif
inst/templates/leftselblue.gif
inst/templates/leftselbluemid.gif
inst/templates/leftselbluesmall.gif
inst/templates/lefttab.gif
inst/templates/lefttabsel.gif
inst/templates/logoBig.png
inst/templates/logoBigNeg.png
inst/templates/logoBigWhite.png
inst/templates/logoSmall.png
inst/templates/lupe.png
inst/templates/lupeSmall.png
inst/templates/lupeSmallbw.png
inst/templates/lupebw.png
inst/templates/midblue.gif
inst/templates/midbluemid.gif
inst/templates/midbluesmall.gif
inst/templates/midselblue.gif
inst/templates/midselbluemid.gif
inst/templates/midselbluesmall.gif
inst/templates/rightblue.gif
inst/templates/rightbluemid.gif
inst/templates/rightbluesmall.gif
inst/templates/rightselblue.gif
inst/templates/rightselbluemid.gif
inst/templates/rightselbluesmall.gif
inst/templates/righttab.gif
inst/templates/righttabsel.gif
inst/templates/sorttable.js
inst/templates/textfileIcon.jpg
inst/templates/wz_tooltip.js
inst/testscreen
inst/testscreen/RA01D1.TXT
inst/testscreen/RA01D2.TXT
inst/testscreen/RA02D1.TXT
inst/testscreen/RA02D2.TXT
inst/testscreen/RB01D1.TXT
inst/testscreen/RB01D2.TXT
inst/testscreen/RB02D1.TXT
inst/testscreen/RB02D2.TXT
inst/testscreen/description.txt
inst/testscreen/plateconf.txt
inst/testscreen/platelist211.txt
inst/testscreen/platelist212.txt
inst/testscreen/platelist213.txt
inst/testscreen/platelist221.txt
inst/testscreen/platelist222.txt
inst/testscreen/platelist233.txt
inst/testscreen/platelist241.txt
inst/testscreen/screenlog.txt
man
man/Bscore.Rd
man/Data.Rd
man/ROC-class.Rd
man/ROC.Rd
man/annotate.Rd
man/batch.Rd
man/bdgpbiomart.Rd
man/buildCellHTS2.Rd
man/cellHTS-class.Rd
man/cellHTS2.Rd
man/configurationAsScreenPlot.Rd
man/configure.Rd
man/convertOldCellHTS.Rd
man/convertWellCoordinates.Rd
man/data-KcViab.Rd
man/data-KcViabSmall.Rd
man/data-dualCh.Rd
man/data-oldKcViabSmall.Rd
man/getDynamicRange.Rd
man/getEnVisionRawData.Rd
man/getMeasureRepAgreement.Rd
man/getTopTable.Rd
man/getZfactor.Rd
man/gseaModule.Rd
man/imageScreen.Rd
man/intensityFiles.Rd
man/normalizePlates.Rd
man/oneRowPerId.Rd
man/plate.Rd
man/plateEffects.Rd
man/plotSpatialEffects.Rd
man/readHTAnalystData.Rd
man/readPlateList.Rd
man/rsa.Rd
man/scoreReplicates.Rd
man/scores2calls.Rd
man/setSettings.Rd
man/spatialNormalization.Rd
man/state.Rd
man/summarizeChannels.Rd
man/summarizeReplicates.Rd
man/templateDescriptionFile.Rd
man/updateCellHTS.Rd
man/wellAnno.Rd
man/write.tabdel.Rd
man/writeReport.Rd
man/writeTab.Rd
tests
tests/test.R
vignettes
vignettes/Rnw
vignettes/Rnw/biomart.Rnw
vignettes/Rnw/biomart.tex
vignettes/cellhts.bib
vignettes/cellhts2.Rnw
vignettes/cellhts2Complete.Rnw
vignettes/twoChannels.Rnw
vignettes/twoWay.Rnw
cellHTS2 documentation built on May 20, 2017, 10:18 p.m.

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