# Analysis of cell-based screens

## Documentation for package ‘cellHTS’ version 1.28.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

annotate | Annotates the gene IDs of a given cellHTS object
annotate.cellHTS | 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
configure.cellHTS | 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
writeTab.cellHTS | Write the data from a cellHTS object to a tab-delimited file