cellHTS: Analysis of cell-based screens

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Analysis of cell-based RNA interference screens.

Author
Wolfgang Huber <huber@ebi.ac.uk>, Ligia Bras <ligia@ebi.ac.uk>, Michael Boutros <m.boutros@dkfz.de>
Date of publication
None
Maintainer
Andrzej OleĊ› <andrzej.oles@embl.de>
License
Artistic-2.0
Version
1.42.0
URLs

View on Bioconductor

Man pages

annotate
Annotates the gene IDs of a given cellHTS object
bdgpbiomart
Dataset with annotation of CG identifiers
Bscore
B score normalization
configure
Configures the plates and plate result files
data-KcViab
A sample cellHTS object - D. melanogaster genome-wide RNAi...
data-KcViabSmall
A sample cellHTS object - D. melanogaster genome-wide RNAi...
getEnVisionRawData
Read a plate file obtain from EnVision Plate Reader
getLibraryPlate
384-well plate assay format to a 96-well plate library format
getMatrix
Create a matrix with replicate data in columns
imageScreen
Experiment-wide quality control plot of a cellHTS object
normalizeChannels
Normalization of dual-channel data and data transformation
normalizePlates
Plate-wise data normalization, and data transformation
oneRowPerId
Rearrange dataframe entries such that there is exactly one...
plotPlateLibrary
Plate plot of the raw data of the four consecutive 96-well...
plotSpatialEffects
Plate plot with the row and column offsets estimated by the B...
print.cellHTS
Printing cellHTS objects
readPlateData
Read a collection of plate reader data files
ROC
Creates an object of class "ROC" which can be plotted as a...
screenMatch
Matching the gene annotation of two screens
summarizeChannels
Normalization and transformation of dual-channel data
summarizeReplicates
Summarizes between normalized replicate values given in a...
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

cellHTS/DESCRIPTION
cellHTS/NAMESPACE
cellHTS/R
cellHTS/R/AllGenerics.R
cellHTS/R/Bscore.R
cellHTS/R/NPI.R
cellHTS/R/POC.R
cellHTS/R/QMbyPlate.R
cellHTS/R/QMexperiment.R
cellHTS/R/calcZscores.R
cellHTS/R/checkColumns.R
cellHTS/R/envisionPlateReader.R
cellHTS/R/getLibraryPlate.R
cellHTS/R/getMatrix.R
cellHTS/R/imageScreen.R
cellHTS/R/makePlot.R
cellHTS/R/methods-cellHTS.R
cellHTS/R/normalizeChannels.R
cellHTS/R/normalizePlates.R
cellHTS/R/oneRowPerId.R
cellHTS/R/plotPlateLibrary.R
cellHTS/R/plotROC.R
cellHTS/R/plotSpatialEffects.R
cellHTS/R/pos2i.R
cellHTS/R/readPlateData.R
cellHTS/R/scaleByPlateMean.R
cellHTS/R/screenMatch.R
cellHTS/R/summarizeChannels.R
cellHTS/R/summarizeReplicates.R
cellHTS/R/tableOutput.R
cellHTS/R/write.tabdel.R
cellHTS/R/writeReport.R
cellHTS/R/zzz.R
cellHTS/build
cellHTS/build/vignette.rds
cellHTS/data
cellHTS/data/KcViab.rda
cellHTS/data/KcViabSmall.rda
cellHTS/data/bdgpbiomart.rda
cellHTS/inst
cellHTS/inst/CITATION
cellHTS/inst/DualChannelScreen
cellHTS/inst/DualChannelScreen/Description.txt
cellHTS/inst/DualChannelScreen/Plateconf.txt
cellHTS/inst/DualChannelScreen/Platelist.txt
cellHTS/inst/DualChannelScreen/RA01D1.TXT
cellHTS/inst/DualChannelScreen/RA01D2.TXT
cellHTS/inst/DualChannelScreen/RA02D1.TXT
cellHTS/inst/DualChannelScreen/RA02D2.TXT
cellHTS/inst/DualChannelScreen/RA03D1.TXT
cellHTS/inst/DualChannelScreen/RA03D2.TXT
cellHTS/inst/DualChannelScreen/RB01D1.TXT
cellHTS/inst/DualChannelScreen/RB01D2.TXT
cellHTS/inst/DualChannelScreen/RB02D1.TXT
cellHTS/inst/DualChannelScreen/RB02D2.TXT
cellHTS/inst/DualChannelScreen/RB03D1.TXT
cellHTS/inst/DualChannelScreen/RB03D2.TXT
cellHTS/inst/DualChannelScreen/Screenlog.txt
cellHTS/inst/EnVisionExample
cellHTS/inst/EnVisionExample/XXX_1500.csv
cellHTS/inst/EnVisionExample/platelist.txt
cellHTS/inst/KcViab
cellHTS/inst/KcViab/Analysis2003.txt
cellHTS/inst/KcViab/Description.txt
cellHTS/inst/KcViab/FT01-G01.txt
cellHTS/inst/KcViab/FT01-G02.txt
cellHTS/inst/KcViab/FT02-G01.txt
cellHTS/inst/KcViab/FT02-G02.txt
cellHTS/inst/KcViab/FT03-G01.txt
cellHTS/inst/KcViab/FT03-G02.txt
cellHTS/inst/KcViab/FT04-G01.txt
cellHTS/inst/KcViab/FT04-G02.txt
cellHTS/inst/KcViab/FT05-G01.txt
cellHTS/inst/KcViab/FT05-G02.txt
cellHTS/inst/KcViab/FT06-G01.txt
cellHTS/inst/KcViab/FT06-G02.txt
cellHTS/inst/KcViab/FT07-G01.txt
cellHTS/inst/KcViab/FT07-G02.txt
cellHTS/inst/KcViab/FT08-G01.txt
cellHTS/inst/KcViab/FT08-G02.txt
cellHTS/inst/KcViab/FT09-G01.txt
cellHTS/inst/KcViab/FT09-G02.txt
cellHTS/inst/KcViab/FT10-G01.txt
cellHTS/inst/KcViab/FT10-G02.txt
cellHTS/inst/KcViab/FT11-G01.txt
cellHTS/inst/KcViab/FT11-G02.txt
cellHTS/inst/KcViab/FT12-G01.txt
cellHTS/inst/KcViab/FT12-G02.txt
cellHTS/inst/KcViab/FT13-G01.txt
cellHTS/inst/KcViab/FT13-G02.txt
cellHTS/inst/KcViab/FT14-G01.txt
cellHTS/inst/KcViab/FT14-G02.txt
cellHTS/inst/KcViab/FT15-G01.txt
cellHTS/inst/KcViab/FT15-G02.txt
cellHTS/inst/KcViab/FT16-G01.txt
cellHTS/inst/KcViab/FT16-G02.txt
cellHTS/inst/KcViab/FT17-G01.txt
cellHTS/inst/KcViab/FT17-G02.txt
cellHTS/inst/KcViab/FT18-G01.txt
cellHTS/inst/KcViab/FT18-G02.txt
cellHTS/inst/KcViab/FT19-G01.txt
cellHTS/inst/KcViab/FT19-G02.txt
cellHTS/inst/KcViab/FT20-G01.txt
cellHTS/inst/KcViab/FT20-G02.txt
cellHTS/inst/KcViab/FT21-G01.txt
cellHTS/inst/KcViab/FT21-G02.txt
cellHTS/inst/KcViab/FT22-G01.txt
cellHTS/inst/KcViab/FT22-G02.txt
cellHTS/inst/KcViab/FT23-G01.txt
cellHTS/inst/KcViab/FT23-G02.txt
cellHTS/inst/KcViab/FT24-G01.txt
cellHTS/inst/KcViab/FT24-G02.txt
cellHTS/inst/KcViab/FT25-G01.txt
cellHTS/inst/KcViab/FT25-G02.txt
cellHTS/inst/KcViab/FT26-G01.txt
cellHTS/inst/KcViab/FT26-G02.txt
cellHTS/inst/KcViab/FT27-G01.txt
cellHTS/inst/KcViab/FT27-G02.txt
cellHTS/inst/KcViab/FT28-G01.txt
cellHTS/inst/KcViab/FT28-G02.txt
cellHTS/inst/KcViab/FT29-G01.txt
cellHTS/inst/KcViab/FT29-G02.txt
cellHTS/inst/KcViab/FT30-G01.txt
cellHTS/inst/KcViab/FT30-G02.txt
cellHTS/inst/KcViab/FT31-G01.txt
cellHTS/inst/KcViab/FT31-G02.txt
cellHTS/inst/KcViab/FT32-G01.txt
cellHTS/inst/KcViab/FT32-G02.txt
cellHTS/inst/KcViab/FT33-G01.txt
cellHTS/inst/KcViab/FT33-G02.txt
cellHTS/inst/KcViab/FT34-G01.txt
cellHTS/inst/KcViab/FT34-G02.txt
cellHTS/inst/KcViab/FT35-G01.txt
cellHTS/inst/KcViab/FT35-G02.txt
cellHTS/inst/KcViab/FT36-G01.txt
cellHTS/inst/KcViab/FT36-G02.txt
cellHTS/inst/KcViab/FT37-G01.txt
cellHTS/inst/KcViab/FT37-G02.txt
cellHTS/inst/KcViab/FT38-G01.txt
cellHTS/inst/KcViab/FT38-G02.txt
cellHTS/inst/KcViab/FT39-G01.txt
cellHTS/inst/KcViab/FT39-G02.txt
cellHTS/inst/KcViab/FT40-G01.txt
cellHTS/inst/KcViab/FT40-G02.txt
cellHTS/inst/KcViab/FT41-G01.txt
cellHTS/inst/KcViab/FT41-G02.txt
cellHTS/inst/KcViab/FT42-G01.txt
cellHTS/inst/KcViab/FT42-G02.txt
cellHTS/inst/KcViab/FT43-G01.txt
cellHTS/inst/KcViab/FT43-G02.txt
cellHTS/inst/KcViab/FT44-G01.txt
cellHTS/inst/KcViab/FT44-G02.txt
cellHTS/inst/KcViab/FT45-G01.txt
cellHTS/inst/KcViab/FT45-G02.txt
cellHTS/inst/KcViab/FT46-G01.txt
cellHTS/inst/KcViab/FT46-G02.txt
cellHTS/inst/KcViab/FT47-G01.txt
cellHTS/inst/KcViab/FT47-G02.txt
cellHTS/inst/KcViab/FT48-G01.txt
cellHTS/inst/KcViab/FT48-G02.txt
cellHTS/inst/KcViab/FT49-G01.txt
cellHTS/inst/KcViab/FT49-G02.txt
cellHTS/inst/KcViab/FT50-G01.txt
cellHTS/inst/KcViab/FT50-G02.txt
cellHTS/inst/KcViab/FT51-G01.txt
cellHTS/inst/KcViab/FT51-G02.txt
cellHTS/inst/KcViab/FT52-G01.txt
cellHTS/inst/KcViab/FT52-G02.txt
cellHTS/inst/KcViab/FT53-G01.txt
cellHTS/inst/KcViab/FT53-G02.txt
cellHTS/inst/KcViab/FT54-G01.txt
cellHTS/inst/KcViab/FT54-G02.txt
cellHTS/inst/KcViab/FT55-G01.txt
cellHTS/inst/KcViab/FT55-G02.txt
cellHTS/inst/KcViab/FT56-G01.txt
cellHTS/inst/KcViab/FT56-G02.txt
cellHTS/inst/KcViab/FT57-G01.txt
cellHTS/inst/KcViab/FT57-G02.txt
cellHTS/inst/KcViab/GeneIDs_Dm_HFA_1.1.txt
cellHTS/inst/KcViab/Plateconf.txt
cellHTS/inst/KcViab/Platelist.txt
cellHTS/inst/KcViab/Screenlog.txt
cellHTS/inst/KcViabSmall
cellHTS/inst/KcViabSmall/Description.txt
cellHTS/inst/KcViabSmall/FT01-G01.txt
cellHTS/inst/KcViabSmall/FT01-G02.txt
cellHTS/inst/KcViabSmall/FT02-G01.txt
cellHTS/inst/KcViabSmall/FT02-G02.txt
cellHTS/inst/KcViabSmall/FT03-G01.txt
cellHTS/inst/KcViabSmall/FT03-G02.txt
cellHTS/inst/KcViabSmall/GeneIDs_Dm_HFAsubset_1.1.txt
cellHTS/inst/KcViabSmall/Plateconf.txt
cellHTS/inst/KcViabSmall/Platelist.txt
cellHTS/inst/KcViabSmall/Screenlog.txt
cellHTS/inst/TwoWayAssay
cellHTS/inst/TwoWayAssay/DHA001LU1.CSV
cellHTS/inst/TwoWayAssay/DHA001LU2.CSV
cellHTS/inst/TwoWayAssay/Description.txt
cellHTS/inst/TwoWayAssay/GeneIDs.txt
cellHTS/inst/TwoWayAssay/Plateconf.txt
cellHTS/inst/TwoWayAssay/Platelist.txt
cellHTS/inst/TwoWayAssay/importData.R
cellHTS/inst/doc
cellHTS/inst/doc/cellhts.R
cellHTS/inst/doc/cellhts.Rnw
cellHTS/inst/doc/cellhts.pdf
cellHTS/inst/doc/twoChannels.R
cellHTS/inst/doc/twoChannels.Rnw
cellHTS/inst/doc/twoChannels.pdf
cellHTS/inst/doc/twoWay.R
cellHTS/inst/doc/twoWay.Rnw
cellHTS/inst/doc/twoWay.pdf
cellHTS/inst/scripts
cellHTS/inst/scripts/cellhtsComplete.Rnw
cellHTS/inst/scripts/makeDatasets.R
cellHTS/man
cellHTS/man/Bscore.Rd
cellHTS/man/ROC.Rd
cellHTS/man/annotate.Rd
cellHTS/man/bdgpbiomart.Rd
cellHTS/man/configure.Rd
cellHTS/man/data-KcViab.Rd
cellHTS/man/data-KcViabSmall.Rd
cellHTS/man/getEnVisionRawData.Rd
cellHTS/man/getLibraryPlate.Rd
cellHTS/man/getMatrix.Rd
cellHTS/man/imageScreen.Rd
cellHTS/man/normalizeChannels.Rd
cellHTS/man/normalizePlates.Rd
cellHTS/man/oneRowPerId.Rd
cellHTS/man/plotPlateLibrary.Rd
cellHTS/man/plotSpatialEffects.Rd
cellHTS/man/print.cellHTS.Rd
cellHTS/man/readPlateData.Rd
cellHTS/man/screenMatch.Rd
cellHTS/man/summarizeChannels.Rd
cellHTS/man/summarizeReplicates.Rd
cellHTS/man/write.tabdel.Rd
cellHTS/man/writeReport.Rd
cellHTS/man/writeTab.Rd
cellHTS/vignettes
cellHTS/vignettes/Rnw
cellHTS/vignettes/Rnw/biomart.Rnw
cellHTS/vignettes/Rnw/biomart.tex
cellHTS/vignettes/cellhts.Rnw
cellHTS/vignettes/cellhts.bib
cellHTS/vignettes/cellhtsComplete.zip
cellHTS/vignettes/twoChannels.Rnw
cellHTS/vignettes/twoWay.Rnw