Entry: Bscore
Aliases: Bscore
Keywords: manip
Description: B score normalization
URL: ../../../library/cellHTS2/html/Bscore.html

Entry: Data
Aliases: Data Data<- Data,cellHTS-method Data<-,cellHTS,array-method
Keywords: manip
Description: Access and replace the assayData slot of a cellHTS object
URL: ../../../library/cellHTS2/html/Data.html

Entry: ROC-class
Aliases: ROC-class show,ROC-method
Keywords: classes
Description: Class that contain data that can be plotted as a ROC curve.
URL: ../../../library/cellHTS2/html/ROC-class.html

Entry: ROC
Aliases: ROC ROC,cellHTS-method plot,ROC,missing-method lines,ROC-method
Keywords: univar
Description: Creates an object of class "ROC" which can be plotted as a ROC curve
URL: ../../../library/cellHTS2/html/ROC.html

Entry: annotate
Aliases: annotate annotate,cellHTS-method
Keywords: 
Description: Annotates the reagents (probes) of a cellHTS object
URL: ../../../library/cellHTS2/html/annotate.html

Entry: batch
Aliases: batch batch<- batch,cellHTS-method batch<-,cellHTS,data.frame-method
Keywords: manip
Description: Access and replace the batch information of a cellHTS object
URL: ../../../library/cellHTS2/html/batch.html

Entry: bdgpbiomart
Aliases: bdgpbiomart
Keywords: datasets
Description: Dataset with annotation of CG identifiers
URL: ../../../library/cellHTS2/html/bdgpbiomart.html

Entry: cellHTS-class
Aliases: cellHTS-class cellHTS class.cellHTS show,cellHTS-method name name<- name,cellHTS-method name<-,cellHTS,character-method initialize,cellHTS-method nbatch nbatch,cellHTS-method compare2cellHTS compare2cellHTS,cellHTS,cellHTS-method meanSdPlot meanSdPlot,cellHTS-method coerce,chtsImage,data.frame-method
Keywords: classes
Description: A class for data from cell-based high-throughput assays performed in plate format.
URL: ../../../library/cellHTS2/html/cellHTS-class.html

Entry: cellHTS2
Aliases: cellHTS2 cellHTS2-package
Keywords: package
Description: cellHTS2 Package Overview
URL: ../../../library/cellHTS2/html/cellHTS2.html

Entry: configurationAsScreenPlot
Aliases: configurationAsScreenPlot
Keywords: 
Description: Screen plot of the plate configuration of a cellHTS object
URL: ../../../library/cellHTS2/html/configurationAsScreenPlot.html

Entry: configure
Aliases: configure configure,cellHTS-method
Keywords: 
Description: Configures the plates and plate result files
URL: ../../../library/cellHTS2/html/configure.html

Entry: convertOldCellHTS
Aliases: convertOldCellHTS
Keywords: 
Description: Convert an old S3 class cellHTS object to the new S4 class cellHTS object
URL: ../../../library/cellHTS2/html/convertOldCellHTS.html

Entry: convertWellCoordinates
Aliases: convertWellCoordinates
Keywords: 
Description: Converts different well identifiers
URL: ../../../library/cellHTS2/html/convertWellCoordinates.html

Entry: KcViab
Aliases: KcViab
Keywords: datasets
Description: A sample cellHTS object - D. melanogaster genome-wide RNAi screen
URL: ../../../library/cellHTS2/html/data-KcViab.html

Entry: KcViabSmall
Aliases: KcViabSmall
Keywords: datasets
Description: A sample cellHTS object - D. melanogaster genome-wide RNAi screen
URL: ../../../library/cellHTS2/html/data-KcViabSmall.html

Entry: dualCh
Aliases: dualCh
Keywords: datasets
Description: A sample cellHTS object containing dual channel data
URL: ../../../library/cellHTS2/html/data-dualCh.html

Entry: oldKcViabSmall
Aliases: oldKcViabSmall
Keywords: datasets
Description: A sample S3 class cellHTS object - D. melanogaster genome-wide RNAi screen
URL: ../../../library/cellHTS2/html/data-oldKcViabSmall.html

Entry: getDynamicRange
Aliases: getDynamicRange
Keywords: manip
Description: Per-plate dynamic range of a cellHTS object
URL: ../../../library/cellHTS2/html/getDynamicRange.html

Entry: getEnVisionRawData
Aliases: getEnVisionRawData getEnVisionCrosstalkCorrectedData
Keywords: manip
Description: Read a plate file obtain from EnVision Plate Reader
URL: ../../../library/cellHTS2/html/getEnVisionRawData.html

Entry: getMeasureRepAgreement
Aliases: getMeasureRepAgreement
Keywords: manip
Description: Measures of agreement between plate replicates from a cellHTS object
URL: ../../../library/cellHTS2/html/getMeasureRepAgreement.html

Entry: getTopTable
Aliases: getTopTable
Keywords: manip
Description: Generate the hit list from a scored cellHTS object
URL: ../../../library/cellHTS2/html/getTopTable.html

Entry: getZfactor
Aliases: getZfactor
Keywords: manip
Description: Per-experiment Z'-factor of a cellHTS object
URL: ../../../library/cellHTS2/html/getZfactor.html

Entry: imageScreen
Aliases: imageScreen
Keywords: manip
Description: Experiment-wide quality control plot of a cellHTS object
URL: ../../../library/cellHTS2/html/imageScreen.html

Entry: intensityFiles
Aliases: intensityFiles intensityFiles,cellHTS-method plateList plateList,cellHTS-method plateConf plateConf,cellHTS-method screenLog screenLog,cellHTS-method screenDesc screenDesc,cellHTS-method
Keywords: manip
Description: Retrieve the contents of the input files used to generate a given cellHTS object.
URL: ../../../library/cellHTS2/html/intensityFiles.html

Entry: normalizePlates
Aliases: normalizePlates plate effects
Keywords: manip
Description: Per-plate data transformation, normalization and variance adjustment
URL: ../../../library/cellHTS2/html/normalizePlates.html

Entry: oneRowPerId
Aliases: oneRowPerId
Keywords: manip
Description: Rearrange dataframe entries such that there is exactly one row per ID.
URL: ../../../library/cellHTS2/html/oneRowPerId.html

Entry: plate
Aliases: plate plate,cellHTS-method pdim pdim,cellHTS-method position position,cellHTS-method well well,cellHTS-method
Keywords: manip
Description: Retrieve information related with the format of a RNAi experiment
URL: ../../../library/cellHTS2/html/plate.html

Entry: plateEffects
Aliases: plateEffects plateEffects,cellHTS-method
Keywords: manip
Description: Access plate effects stored in a cellHTS object.
URL: ../../../library/cellHTS2/html/plateEffects.html

Entry: plotSpatialEffects
Aliases: plotSpatialEffects
Keywords: manip
Description: Plate plot with the row and column offsets estimated by the a spatial normalization method
URL: ../../../library/cellHTS2/html/plotSpatialEffects.html

Entry: readHTAnalystData
Aliases: readHTAnalystData
Keywords: manip
Description: Read a set of plate results obtained from a HTanalyser plate reader
URL: ../../../library/cellHTS2/html/readHTAnalystData.html

Entry: readPlateList
Aliases: readPlateList
Keywords: manip
Description: Read a collection of plate reader data files
URL: ../../../library/cellHTS2/html/readPlateList.html

Entry: scoreReplicates
Aliases: scoreReplicates
Keywords: manip
Description: Scores normalized replicate values given in a cellHTS object
URL: ../../../library/cellHTS2/html/scoreReplicates.html

Entry: scores2calls
Aliases: scores2calls
Keywords: manip
Description: Sigmoidal transformation of the score values stored in a cellHTS object obtaining the call values for each probe.
URL: ../../../library/cellHTS2/html/scores2calls.html

Entry: spatialNormalization
Aliases: spatialNormalization
Keywords: manip
Description: Spatial normalization
URL: ../../../library/cellHTS2/html/spatialNormalization.html

Entry: state
Aliases: state state,cellHTS-method
Keywords: manip
Description: Retrieve the state of a cellHTS object.
URL: ../../../library/cellHTS2/html/state.html

Entry: summarizeChannels
Aliases: summarizeChannels
Keywords: manip
Description: Summarization of dual-channel data
URL: ../../../library/cellHTS2/html/summarizeChannels.html

Entry: summarizeReplicates
Aliases: summarizeReplicates
Keywords: manip
Description: Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe
URL: ../../../library/cellHTS2/html/summarizeReplicates.html

Entry: templateDescriptionFile
Aliases: templateDescriptionFile
Keywords: manip
Description: Creates a template description file for an RNAi experiment
URL: ../../../library/cellHTS2/html/templateDescriptionFile.html

Entry: updateCellHTS
Aliases: updateCellHTS
Keywords: 
Description: Update old serialized cellHTS objects.
URL: ../../../library/cellHTS2/html/updateCellHTS.html

Entry: wellAnno
Aliases: wellAnno wellAnno,cellHTS-method geneAnno geneAnno,cellHTS-method
Keywords: manip
Description: Access the annotation from a cellHTS object.
URL: ../../../library/cellHTS2/html/wellAnno.html

Entry: write.tabdel
Aliases: write.tabdel
Keywords: manip
Description: Wrapper to function 'write.table' used to write data to a tab-delimited file
URL: ../../../library/cellHTS2/html/write.tabdel.html

Entry: writeReport
Aliases: writeReport
Keywords: manip
Description: Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS experiment
URL: ../../../library/cellHTS2/html/writeReport.html

Entry: writeTab
Aliases: writeTab writeTab,cellHTS-method
Keywords: manip
Description: Write the data from a cellHTS object to a tab-delimited file
URL: ../../../library/cellHTS2/html/writeTab.html
