Entry: BScore
Aliases: BScore
Keywords: manip
Description: BScore normalization
URL: ../../../library/RNAither/html/BScore.html

Entry: DRQualControl
Aliases: DRQualControl
Keywords: device
Description: Computing the dynamic range
URL: ../../../library/RNAither/html/DRQualControl.html

Entry: LiWongRank
Aliases: LiWongRank
Keywords: manip
Description: Li Wong rank / invariant probeset normalization
URL: ../../../library/RNAither/html/LiWongRank.html

Entry: MannWhitney
Aliases: MannWhitney
Keywords: manip
Description: Perform a Mann-Whitney test
URL: ../../../library/RNAither/html/MannWhitney.html

Entry: RNAither-package
Aliases: RNAither-package RNAither
Keywords: 
Description: Statistical analysis of high-throughput RNAi screens
URL: ../../../library/RNAither/html/RNAither-package.html

Entry: RankProduct
Aliases: RankProduct
Keywords: univar
Description: Perform a Rank Product test
URL: ../../../library/RNAither/html/RankProduct.html

Entry: SNRQualControl
Aliases: SNRQualControl
Keywords: arith
Description: Computing the SNR
URL: ../../../library/RNAither/html/SNRQualControl.html

Entry: Ttest
Aliases: Ttest
Keywords: univar
Description: Perform a Student's t-test
URL: ../../../library/RNAither/html/Ttest.html

Entry: ZPRIMEQualControl
Aliases: ZPRIMEQualControl
Keywords: arith
Description: Computing the Z' factor
URL: ../../../library/RNAither/html/ZPRIMEQualControl.html

Entry: ZScore
Aliases: ZScore
Keywords: manip
Description: ZScore normalization
URL: ../../../library/RNAither/html/ZScore.html

Entry: ZScorePerScreen
Aliases: ZScorePerScreen
Keywords: manip
Description: ZScore normalization per experiment
URL: ../../../library/RNAither/html/ZScorePerScreen.html

Entry: ZScorePlot
Aliases: ZScorePlot
Keywords: device
Description: Plot normalized intensity values per well
URL: ../../../library/RNAither/html/ZScorePlot.html

Entry: ZScorePlotTwo
Aliases: ZScorePlotTwo
Keywords: device
Description: Plot signal intensities per well (II)
URL: ../../../library/RNAither/html/ZScorePlotTwo.html

Entry: channelPlot
Aliases: channelPlot
Keywords: device
Description: Plot signal channels against each other
URL: ../../../library/RNAither/html/channelPlot.html

Entry: closestToZero
Aliases: closestToZero
Keywords: arith
Description: Return the replicate value closest to zero
URL: ../../../library/RNAither/html/closestToZero.html

Entry: compareHits
Aliases: compareHits
Keywords: arith
Description: Searching for common hits between different scoring methods
URL: ../../../library/RNAither/html/compareHits.html

Entry: compareReplicaPlates
Aliases: compareReplicaPlates
Keywords: arith
Description: Compare replica plates
URL: ../../../library/RNAither/html/compareReplicaPlates.html

Entry: compareReplicateSD
Aliases: compareReplicateSD
Keywords: arith device
Description: Plot the standard deviation of replicates
URL: ../../../library/RNAither/html/compareReplicateSD.html

Entry: compareReplicateSDPerScreen
Aliases: compareReplicateSDPerScreen
Keywords: arith device
Description: Plot the standard deviation of replicates for each experiment
URL: ../../../library/RNAither/html/compareReplicateSDPerScreen.html

Entry: compareReplicates
Aliases: compareReplicates
Keywords: arith device
Description: Compare replicate values
URL: ../../../library/RNAither/html/compareReplicates.html

Entry: controlDensity
Aliases: controlDensity
Keywords: device
Description: Plotting the control density
URL: ../../../library/RNAither/html/controlDensity.html

Entry: controlDensityPerPlate
Aliases: controlDensityPerPlate
Keywords: device
Description: Plotting the control density per plate
URL: ../../../library/RNAither/html/controlDensityPerPlate.html

Entry: controlDensityPerScreen
Aliases: controlDensityPerScreen
Keywords: device
Description: Plotting the control density per experiment
URL: ../../../library/RNAither/html/controlDensityPerScreen.html

Entry: controlNorm
Aliases: controlNorm
Keywords: manip
Description: Normalization on controls
URL: ../../../library/RNAither/html/controlNorm.html

Entry: createSubset
Aliases: createSubset
Keywords: arith
Description: Creating a subset of a dataset according to a certain column value
URL: ../../../library/RNAither/html/createSubset.html

Entry: dataset
Aliases: dataset
Keywords: datasets
Description: a typical example RNAi dataset
URL: ../../../library/RNAither/html/dataset.html

Entry: datasetDrosophila
Aliases: datasetDrosophila
Keywords: datasets
Description: Genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.
URL: ../../../library/RNAither/html/datasetDrosophila.html

Entry: discardLabtek
Aliases: discardLabtek
Keywords: arith
Description: Remove a complete plate from the analysis
URL: ../../../library/RNAither/html/discardLabtek.html

Entry: discardWells
Aliases: discardWells
Keywords: arith
Description: Remove wells from the analysis
URL: ../../../library/RNAither/html/discardWells.html

Entry: divNorm
Aliases: divNorm
Keywords: manip
Description: Mean, median, ... , normalization
URL: ../../../library/RNAither/html/divNorm.html

Entry: divideChannels
Aliases: divideChannels
Keywords: manip arith
Description: Divide channel values
URL: ../../../library/RNAither/html/divideChannels.html

Entry: eraseDataSetColumn
Aliases: eraseDataSetColumn
Keywords: manip
Description: Remove columns from dataset
URL: ../../../library/RNAither/html/eraseDataSetColumn.html

Entry: findReplicates
Aliases: findReplicates
Keywords: methods
Description: Find all replicates of a certain siRNA/gene in a dataset
URL: ../../../library/RNAither/html/findReplicates.html

Entry: furthestFromZero
Aliases: furthestFromZero
Keywords: arith
Description: Return the replicate value furthest from zero
URL: ../../../library/RNAither/html/furthestFromZero.html

Entry: generateDatasetFile
Aliases: generateDatasetFile
Keywords: datagen
Description: Generate Dataset File
URL: ../../../library/RNAither/html/generateDatasetFile.html

Entry: generateRepMatNoFilter
Aliases: generateRepMatNoFilter
Keywords: arith
Description: Generate a matrix of replicates (II)
URL: ../../../library/RNAither/html/generateRepMatNoFilter.html

Entry: generateReplicateMat
Aliases: generateReplicateMat
Keywords: arith
Description: Generate a matrix of replicates
URL: ../../../library/RNAither/html/generateReplicateMat.html

Entry: gseaAnalysis
Aliases: gseaAnalysis
Keywords: database datagen
Description: Perform a GSEA analysis of a list of genes
URL: ../../../library/RNAither/html/gseaAnalysis.html

Entry: header
Aliases: header
Keywords: datasets
Description: a typical header of an example RNAi dataset
URL: ../../../library/RNAither/html/header.html

Entry: headerDrosophila
Aliases: headerDrosophila
Keywords: datasets
Description: the header of the genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.
URL: ../../../library/RNAither/html/headerDrosophila.html

Entry: hitselectionPval
Aliases: hitselectionPval
Keywords: arith
Description: Selecting hits according to p-values
URL: ../../../library/RNAither/html/hitselectionPval.html

Entry: hitselectionZscore
Aliases: hitselectionZscore
Keywords: arith
Description: Selecting hits according to ZScores
URL: ../../../library/RNAither/html/hitselectionZscore.html

Entry: hitselectionZscorePval
Aliases: hitselectionZscorePval
Keywords: arith
Description: Selecting hits according to ZScores and p-values
URL: ../../../library/RNAither/html/hitselectionZscorePval.html

Entry: incorporatepValVec
Aliases: incorporatepValVec
Keywords: manip
Description: Incorporate a vector of p-values into a dataset
URL: ../../../library/RNAither/html/incorporatepValVec.html

Entry: indexSubset
Aliases: indexSubset
Keywords: arith
Description: Saving the indexes of a subset in the main dataset
URL: ../../../library/RNAither/html/indexSubset.html

Entry: joinDatasetFiles
Aliases: joinDatasetFiles
Keywords: datagen
Description: Join dataset files
URL: ../../../library/RNAither/html/joinDatasetFiles.html

Entry: joinDatasets
Aliases: joinDatasets
Keywords: datagen
Description: Join datasets
URL: ../../../library/RNAither/html/joinDatasets.html

Entry: lowessNorm
Aliases: lowessNorm
Keywords: manip
Description: Lowess normalization
URL: ../../../library/RNAither/html/lowessNorm.html

Entry: mainAnalysis
Aliases: mainAnalysis
Keywords: dplot device arith manip database methods univar datagen misc utilities
Description: Wrapper function for full automated analysis
URL: ../../../library/RNAither/html/mainAnalysis.html

Entry: makeBoxplot4PlateType
Aliases: makeBoxplot4PlateType
Keywords: device
Description: Generate a boxplot of the data per plate
URL: ../../../library/RNAither/html/makeBoxplot4PlateType.html

Entry: makeBoxplotControls
Aliases: makeBoxplotControls
Keywords: device
Description: Generate a boxplot of the data vs. the controls
URL: ../../../library/RNAither/html/makeBoxplotControls.html

Entry: makeBoxplotControlsPerPlate
Aliases: makeBoxplotControlsPerPlate
Keywords: device
Description: Generate a boxplot of the data vs. the controls for each plate
URL: ../../../library/RNAither/html/makeBoxplotControlsPerPlate.html

Entry: makeBoxplotControlsPerScreen
Aliases: makeBoxplotControlsPerScreen
Keywords: device
Description: Generate a boxplot of the data vs. the controls for each experiment
URL: ../../../library/RNAither/html/makeBoxplotControlsPerScreen.html

Entry: makeBoxplotPerPlate
Aliases: makeBoxplotPerPlate
Keywords: device
Description: Generate a boxplot of the data per plate
URL: ../../../library/RNAither/html/makeBoxplotPerPlate.html

Entry: makeBoxplotPerScreen
Aliases: makeBoxplotPerScreen
Keywords: device
Description: Generate a boxplot of the data per experiment
URL: ../../../library/RNAither/html/makeBoxplotPerScreen.html

Entry: multTestAdjust
Aliases: multTestAdjust
Keywords: manip
Description: Adjust p-values for multiple testing
URL: ../../../library/RNAither/html/multTestAdjust.html

Entry: numCellQualControl
Aliases: numCellQualControl
Keywords: device arith
Description: Quality control of the number of cells
URL: ../../../library/RNAither/html/numCellQualControl.html

Entry: orderGeneIDs
Aliases: orderGeneIDs
Keywords: arith
Description: Order a dataset
URL: ../../../library/RNAither/html/orderGeneIDs.html

Entry: pValVec1
Aliases: pValVec1
Keywords: datasets
Description: A vector of p-values after a median normalization and a t-test
URL: ../../../library/RNAither/html/pValVec1.html

Entry: pValVec2
Aliases: pValVec2
Keywords: datasets
Description: A vector of p-values after a Mann-Whitney test
URL: ../../../library/RNAither/html/pValVec2.html

Entry: percCellQualControl
Aliases: percCellQualControl
Keywords: device arith
Description: Quality control of the percentage of cells
URL: ../../../library/RNAither/html/percCellQualControl.html

Entry: plotBar
Aliases: plotBar
Keywords: device
Description: Plot signal intensities per well
URL: ../../../library/RNAither/html/plotBar.html

Entry: plotControlHisto
Aliases: plotControlHisto
Keywords: device
Description: Plot a histogram of the data values and controls
URL: ../../../library/RNAither/html/plotControlHisto.html

Entry: plotControlHistoPerplate
Aliases: plotControlHistoPerplate
Keywords: device
Description: Plot a histogram of the data values and controls per plate
URL: ../../../library/RNAither/html/plotControlHistoPerplate.html

Entry: plotControlHistoPerscreen
Aliases: plotControlHistoPerscreen
Keywords: device
Description: Plot a histogram of the data values and controls per experiment
URL: ../../../library/RNAither/html/plotControlHistoPerscreen.html

Entry: plotHisto
Aliases: plotHisto
Keywords: device
Description: Plot a histogram of the data values
URL: ../../../library/RNAither/html/plotHisto.html

Entry: plotHistoPerplate
Aliases: plotHistoPerplate
Keywords: device
Description: Plot a histogram of the data values per plate
URL: ../../../library/RNAither/html/plotHistoPerplate.html

Entry: plotHistoPerscreen
Aliases: plotHistoPerscreen
Keywords: device
Description: Plot a histogram of the data values per experiment
URL: ../../../library/RNAither/html/plotHistoPerscreen.html

Entry: plotQQ
Aliases: plotQQ
Keywords: device
Description: Make a QQ plot
URL: ../../../library/RNAither/html/plotQQ.html

Entry: plotQQperplate
Aliases: plotQQperplate
Keywords: device
Description: Make a QQ plot per plate
URL: ../../../library/RNAither/html/plotQQperplate.html

Entry: plotQQperscreen
Aliases: plotQQperscreen
Keywords: device
Description: Make a QQ plot per experiment
URL: ../../../library/RNAither/html/plotQQperscreen.html

Entry: quantileNormalization
Aliases: quantileNormalization
Keywords: manip
Description: Quantile normalization
URL: ../../../library/RNAither/html/quantileNormalization.html

Entry: replicatesCV
Aliases: replicatesCV
Keywords: arith
Description: Compute the correlation of variation (CV)
URL: ../../../library/RNAither/html/replicatesCV.html

Entry: replicatesSpearmancor
Aliases: replicatesSpearmancor
Keywords: arith
Description: Compute the correlation coefficient betwenn replicates or experiments
URL: ../../../library/RNAither/html/replicatesSpearmancor.html

Entry: rms
Aliases: rms
Keywords: arith
Description: Compute the replicate root mean square
URL: ../../../library/RNAither/html/rms.html

Entry: saveDataset
Aliases: saveDataset
Keywords: IO
Description: Save the normalized dataset into a dataset text file
URL: ../../../library/RNAither/html/saveDataset.html

Entry: saveOldIntensityColumns
Aliases: saveOldIntensityColumns
Keywords: datagen manip
Description: Save old intensity value columns
URL: ../../../library/RNAither/html/saveOldIntensityColumns.html

Entry: savepValVec
Aliases: savepValVec
Keywords: datagen IO
Description: Save p-values to file
URL: ../../../library/RNAither/html/savepValVec.html

Entry: scoredDataset1
Aliases: scoredDataset1
Keywords: datasets
Description: A dataset containing an additional column showing the p-values, after a median normalization and a t-test
URL: ../../../library/RNAither/html/scoredDataset1.html

Entry: scoredDataset2
Aliases: scoredDataset2
Keywords: datasets
Description: A dataset containing an additional column showing the p-values after a Mann-Whitney test
URL: ../../../library/RNAither/html/scoredDataset2.html

Entry: spatialDistrib
Aliases: spatialDistrib
Keywords: device
Description: Generate spatial plots of intensity values
URL: ../../../library/RNAither/html/spatialDistrib.html

Entry: spatialDistribHits
Aliases: spatialDistribHits
Keywords: device
Description: Plotting the spatial distribution of the hits
URL: ../../../library/RNAither/html/spatialDistribHits.html

Entry: subtractBackground
Aliases: subtractBackground
Keywords: manip
Description: Background substraction
URL: ../../../library/RNAither/html/subtractBackground.html

Entry: sumChannels
Aliases: sumChannels
Keywords: manip
Description: Summarize channels
URL: ../../../library/RNAither/html/sumChannels.html

Entry: summarizeReps
Aliases: summarizeReps
Keywords: arith
Description: Generate a new dataset with summarized replicates
URL: ../../../library/RNAither/html/summarizeReps.html

Entry: summarizeRepsNoFiltering
Aliases: summarizeRepsNoFiltering
Keywords: arith
Description: Generate a new dataset with summarized replicates
URL: ../../../library/RNAither/html/summarizeRepsNoFiltering.html

Entry: trim
Aliases: trim
Keywords: arith
Description: Compute the replicate mean with trimmed values
URL: ../../../library/RNAither/html/trim.html

Entry: varAdjust
Aliases: varAdjust
Keywords: manip
Description: Variance adjustment
URL: ../../../library/RNAither/html/varAdjust.html

Entry: vennDiag
Aliases: vennDiag
Keywords: device
Description: Plotting a Venn Diagram to compare hits
URL: ../../../library/RNAither/html/vennDiag.html

Entry: volcanoPlot
Aliases: volcanoPlot
Keywords: device univar
Description: Making a volcano plot
URL: ../../../library/RNAither/html/volcanoPlot.html
