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

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>
Date of publicationNone
MaintainerJoseph Barry <joseph.barry@embl.de>
LicenseArtistic-2.0
Version2.38.0
http://www.dkfz.de/signaling
http://www.ebi.ac.uk/huber

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

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