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

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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.

Author
Ligia Bras, Wolfgang Huber <whuber@embl.de>, Michael Boutros <m.boutros@dkfz.de>, Gregoire Pau <gpau@embl.de>, Florian Hahne <florian.hahne@novartis.com>
Date of publication
None
Maintainer
Joseph Barry <joseph.barry@embl.de>
License
Artistic-2.0
Version
2.38.0
URLs

View on Bioconductor

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...

Files in this package

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