cellHTS: Analysis of cell-based screens

Analysis of cell-based RNA interference screens.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cellHTS")
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...

Functions

annotate Man page
annotate.cellHTS Man page
bdgpbiomart Man page
Bscore Man page
configure Man page
configure.cellHTS Man page
getEnVisionCrosstalkCorrectedData Man page
getEnVisionRawData Man page
getLibraryPlate Man page
getMatrix Man page
imageScreen Man page
KcViab Man page
KcViabSmall Man page
lines.ROC Man page
normalizeChannels Man page
normalizePlates Man page
oneRowPerId Man page
plate effects Man page
plotPlateLibrary Man page
plot.ROC Man page
plotSpatialEffects Man page
print.cellHTS Man page
readPlateData Man page
ROC Man page
screenMatch Man page
summarizeChannels Man page
summarizeReplicates Man page
writeReport Man page
writeTab Man page
writeTab.cellHTS Man page
write.tabdel Man page

Files

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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