cellHTS: Analysis of cell-based screens

Analysis of cell-based RNA interference screens.

AuthorWolfgang Huber <huber@ebi.ac.uk>, Ligia Bras <ligia@ebi.ac.uk>, Michael Boutros <m.boutros@dkfz.de>
Date of publicationNone
MaintainerAndrzej OleĊ› <andrzej.oles@embl.de>
LicenseArtistic-2.0
Version1.42.0
http://www.dkfz.de/signaling
http://www.ebi.ac.uk/huber

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

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