Analysis of cell-based screens


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Documentation for package ‘cellHTS’ version 1.12.0

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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
getEnVisionCrosstalkCorrectedData Read a plate file obtain from EnVision Plate Reader
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
KcViab A sample cellHTS object - D. melanogaster genome-wide RNAi screen
KcViabSmall A sample cellHTS object - D. melanogaster genome-wide RNAi screen
lines.ROC Creates an object of class "ROC" which can be plotted as a ROC curve
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 row per ID.
plate effects Plate-wise data normalization, and data transformation
plot.ROC Creates an object of class "ROC" which can be plotted as a ROC curve
plotPlateLibrary Plate plot of the raw data of the four consecutive 96-well plates of a given 384-well plate
plotSpatialEffects Plate plot with the row and column offsets estimated by the B score method
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 ROC curve
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 cellHTS object, obtaining a single z-score for each probe
write.tabdel Wrapper to function 'write.table' used to write data to a tab-delimited file
writeReport Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS object
writeTab Write the data from a cellHTS object to a tab-delimited file