RNAither: Statistical analysis of high-throughput RNAi screens
Version 2.24.0

RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.

Browse man pages Browse package API and functions Browse package files

AuthorNora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Bioconductor views Annotation CellBasedAssays GO Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerLars Kaderali <lars.kaderali@uni-greifswald.de>
LicenseArtistic-2.0
Version2.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RNAither")

Man pages

BScore: BScore normalization
channelPlot: Plot signal channels against each other
closestToZero: Return the replicate value closest to zero
compareHits: Searching for common hits between different scoring methods
compareReplicaPlates: Compare replica plates
compareReplicates: Compare replicate values
compareReplicateSD: Plot the standard deviation of replicates
compareReplicateSDPerScreen: Plot the standard deviation of replicates for each experiment
controlDensity: Plotting the control density
controlDensityPerPlate: Plotting the control density per plate
controlDensityPerScreen: Plotting the control density per experiment
controlNorm: Normalization on controls
createSubset: Creating a subset of a dataset according to a certain column...
dataset: a typical example RNAi dataset
datasetDrosophila: Genome-wide RNAi screen of cell viability in Drosophila Kc167...
discardLabtek: Remove a complete plate from the analysis
discardWells: Remove wells from the analysis
divideChannels: Divide channel values
divNorm: Mean, median, ... , normalization
DRQualControl: Computing the dynamic range
eraseDataSetColumn: Remove columns from dataset
findReplicates: Find all replicates of a certain siRNA/gene in a dataset
furthestFromZero: Return the replicate value furthest from zero
generateDatasetFile: Generate Dataset File
generateReplicateMat: Generate a matrix of replicates
generateRepMatNoFilter: Generate a matrix of replicates (II)
gseaAnalysis: Perform a GSEA analysis of a list of genes
header: a typical header of an example RNAi dataset
headerDrosophila: the header of the genome-wide RNAi screen of cell viability...
hitselectionPval: Selecting hits according to p-values
hitselectionZscore: Selecting hits according to ZScores
hitselectionZscorePval: Selecting hits according to ZScores and p-values
incorporatepValVec: Incorporate a vector of p-values into a dataset
indexSubset: Saving the indexes of a subset in the main dataset
joinDatasetFiles: Join dataset files
joinDatasets: Join datasets
LiWongRank: Li Wong rank / invariant probeset normalization
lowessNorm: Lowess normalization
mainAnalysis: Wrapper function for full automated analysis
makeBoxplot4PlateType: Generate a boxplot of the data per plate
makeBoxplotControls: Generate a boxplot of the data vs. the controls
makeBoxplotControlsPerPlate: Generate a boxplot of the data vs. the controls for each...
makeBoxplotControlsPerScreen: Generate a boxplot of the data vs. the controls for each...
makeBoxplotPerPlate: Generate a boxplot of the data per plate
makeBoxplotPerScreen: Generate a boxplot of the data per experiment
MannWhitney: Perform a Mann-Whitney test
multTestAdjust: Adjust p-values for multiple testing
numCellQualControl: Quality control of the number of cells
orderGeneIDs: Order a dataset
percCellQualControl: Quality control of the percentage of cells
plotBar: Plot signal intensities per well
plotControlHisto: Plot a histogram of the data values and controls
plotControlHistoPerplate: Plot a histogram of the data values and controls per plate
plotControlHistoPerscreen: Plot a histogram of the data values and controls per...
plotHisto: Plot a histogram of the data values
plotHistoPerplate: Plot a histogram of the data values per plate
plotHistoPerscreen: Plot a histogram of the data values per experiment
plotQQ: Make a QQ plot
plotQQperplate: Make a QQ plot per plate
plotQQperscreen: Make a QQ plot per experiment
pValVec1: A vector of p-values after a median normalization and a...
pValVec2: A vector of p-values after a Mann-Whitney test
quantileNormalization: Quantile normalization
RankProduct: Perform a Rank Product test
replicatesCV: Compute the correlation of variation (CV)
replicatesSpearmancor: Compute the correlation coefficient betwenn replicates or...
rms: Compute the replicate root mean square
rnaither: Wrapper function for full automated analysis
RNAither-package: Statistical analysis of high-throughput RNAi screens
saveDataset: Save the normalized dataset into a dataset text file
saveOldIntensityColumns: Save old intensity value columns
savepValVec: Save p-values to file
scoredDataset1: A dataset containing an additional column showing the...
scoredDataset2: A dataset containing an additional column showing the...
SNRQualControl: Computing the SNR
spatialDistrib: Generate spatial plots of intensity values
spatialDistribHits: Plotting the spatial distribution of the hits
subtractBackground: Background substraction
sumChannels: Summarize channels
summarizeReps: Generate a new dataset with summarized replicates
summarizeRepsNoFiltering: Generate a new dataset with summarized replicates
trim: Compute the replicate mean with trimmed values
Ttest: Perform a Student's t-test
varAdjust: Variance adjustment
vennDiag: Plotting a Venn Diagram to compare hits
volcanoPlot: Making a volcano plot
ZPRIMEQualControl: Computing the Z' factor
ZScore: ZScore normalization
ZScorePerScreen: ZScore normalization per experiment
ZScorePlot: Plot normalized intensity values per well
ZScorePlotTwo: Plot signal intensities per well (II)

Functions

BScore Man page Source code
DRQualControl Man page Source code
GOannotate Source code
LiWongRank Man page Source code
MannWhitney Man page Source code
PlotSpatialDistrib Source code
RNAither Man page
RNAither-package Man page
RankProduct Man page Source code
SNRQualControl Man page Source code
Ttest Man page Source code
ZPRIMEQualControl Man page Source code
ZPrime Source code
ZScore Man page Source code
ZScorePerScreen Man page Source code
ZScorePlot Man page Source code
ZScorePlotTwo Man page Source code
attempt_fix Source code
channelPlot Man page Source code
check_layout_consistent Source code
closestToZero Man page Source code
compareHits Man page Source code
compareReplicaPlates Man page Source code
compareReplicateSD Man page Source code
compareReplicateSDPerScreen Man page Source code
compareReplicates Man page Source code
controlDensity Man page Source code
controlDensityPerPlate Man page Source code
controlDensityPerScreen Man page Source code
controlNorm Man page Source code
createReplicateMatrix Source code
createSubset Man page Source code
dataset Man page
datasetDrosophila Man page
discardLabtek Man page Source code
discardWells Man page Source code
divNorm Man page Source code
divideChannels Man page Source code
doCtrlNorm Source code
doPercNegNorm Source code
doPocNorm Source code
dynamicRange Source code
eraseDataSetColumn Man page Source code
findReplicates Man page Source code
function1 Source code
function2 Source code
function2b Source code
function2c Source code
function3 Source code
function4a Source code
function4b Source code
function5 Source code
function6 Source code
function7 Source code
furthestFromZero Man page Source code
geneNameAnno Source code
generateDatasetFile Man page Source code
generateRepMatNoFilter Man page Source code
generateReplicateMat Man page Source code
gseaAnalysis Man page Source code
gseaAnalysisPt1 Source code
gseaAnalysisPt2 Source code
gseaTableFunc Source code
header Man page
headerDrosophila Man page
hitselectionPval Man page Source code
hitselectionZscore Man page Source code
hitselectionZscorePval Man page Source code
incorporatepValVec Man page Source code
indexSubset Man page Source code
joinDatasetFiles Man page Source code
joinDatasets Man page Source code
listChooseIndex Source code
lowessNorm Man page Source code
mainAnalysis Man page Source code
makeBoxplot4PlateType Man page Source code
makeBoxplotControls Man page Source code
makeBoxplotControlsPerPlate Man page Source code
makeBoxplotControlsPerScreen Man page Source code
makeBoxplotOverview Source code
makeBoxplotPerPlate Man page Source code
makeBoxplotPerScreen Man page Source code
makeCorrPlots Source code
makeCtrlBoxPlot Source code
makeCtrlDensityPlot Source code
makePlateDetailPlots Source code
makeQCPlots Source code
makeScreenOverview Source code
makefullbarplot Source code
makevolcanoplot Source code
multTestAdjust Man page Source code
numCellQualControl Man page Source code
orderGeneIDs Man page Source code
pValVec1 Man page
pValVec2 Man page
percCellQualControl Man page Source code
plotBar Man page Source code
plotBarGeruest Source code
plotControlHisto Man page Source code
plotControlHistoPerplate Man page Source code
plotControlHistoPerscreen Man page Source code
plotHisto Man page Source code
plotHistoPerplate Man page Source code
plotHistoPerscreen Man page Source code
plotQQ Man page Source code
plotQQperplate Man page Source code
plotQQperscreen Man page Source code
plothist Source code
plotmybar Source code
plotqq Source code
plotscatter Source code
quantileNormalization Man page Source code
reorderdata Source code
replicatesCV Man page Source code
replicatesSpearmancor Man page Source code
rms Man page Source code
rnaither Man page Source code
saveDataset Man page Source code
saveOldIntensityColumns Man page Source code
savepValVec Man page Source code
scoredDataset1 Man page
scoredDataset2 Man page
spatialDistrib Man page Source code
spatialDistribHits Man page Source code
subtractBackground Man page Source code
sumChannels Man page Source code
summarizeReplicates Source code
summarizeReps Man page Source code
summarizeRepsNoFiltering Man page Source code
trim Man page Source code
varAdjust Man page Source code
vennDiag Man page Source code
vennDiagfunc Source code
volcanoPlot Man page Source code
whtml Source code
writeSummaryHtml Source code
writegoresults Source code
writehitlist Source code
ylabCompute Source code

Files

DESCRIPTION
NAMESPACE
R
R/GSEA.R
R/general_functions.R
R/generate_dataset_file.R
R/normalization.R
R/odbc_connect.R
R/quality_control.R
R/rnaistat.R
R/stattest.R
R/wrapper.R
build
build/vignette.rds
data
data/datasetDrosophila.rda
data/exampleDataset.rda
data/exampleHeader.rda
data/headerDrosophila.rda
data/pValVec1.rda
data/pValVec2.rda
data/scoredDataset1.rda
data/scoredDataset2.rda
inst
inst/doc
inst/doc/vignetteRNAither.R
inst/doc/vignetteRNAither.Rnw
inst/doc/vignetteRNAither.pdf
inst/extdata
inst/extdata/CITATION
man
man/BScore.Rd
man/DRQualControl.Rd
man/LiWongRank.Rd
man/MannWhitney.Rd
man/RNAither-package.Rd
man/RankProduct.Rd
man/SNRQualControl.Rd
man/Ttest.Rd
man/ZPRIMEQualControl.Rd
man/ZScore.Rd
man/ZScorePerScreen.Rd
man/ZScorePlot.Rd
man/ZScorePlotTwo.Rd
man/channelPlot.Rd
man/closestToZero.Rd
man/compareHits.Rd
man/compareReplicaPlates.Rd
man/compareReplicateSD.Rd
man/compareReplicateSDPerScreen.Rd
man/compareReplicates.Rd
man/controlDensity.Rd
man/controlDensityPerPlate.Rd
man/controlDensityPerScreen.Rd
man/controlNorm.Rd
man/createSubset.Rd
man/dataset.Rd
man/datasetDrosophila.Rd
man/discardLabtek.Rd
man/discardWells.Rd
man/divNorm.Rd
man/divideChannels.Rd
man/eraseDataSetColumn.Rd
man/findReplicates.Rd
man/furthestFromZero.Rd
man/generateDatasetFile.Rd
man/generateRepMatNoFilter.Rd
man/generateReplicateMat.Rd
man/gseaAnalysis.Rd
man/header.Rd
man/headerDrosophila.Rd
man/hitselectionPval.Rd
man/hitselectionZscore.Rd
man/hitselectionZscorePval.Rd
man/incorporatepValVec.Rd
man/indexSubset.Rd
man/joinDatasetFiles.Rd
man/joinDatasets.Rd
man/lowessNorm.Rd
man/mainAnalysis.Rd
man/makeBoxplot4PlateType.Rd
man/makeBoxplotControls.Rd
man/makeBoxplotControlsPerPlate.Rd
man/makeBoxplotControlsPerScreen.Rd
man/makeBoxplotPerPlate.Rd
man/makeBoxplotPerScreen.Rd
man/multTestAdjust.Rd
man/numCellQualControl.Rd
man/orderGeneIDs.Rd
man/pValVec1.Rd
man/pValVec2.Rd
man/percCellQualControl.Rd
man/plotBar.Rd
man/plotControlHisto.Rd
man/plotControlHistoPerplate.Rd
man/plotControlHistoPerscreen.Rd
man/plotHisto.Rd
man/plotHistoPerplate.Rd
man/plotHistoPerscreen.Rd
man/plotQQ.Rd
man/plotQQperplate.Rd
man/plotQQperscreen.Rd
man/quantileNormalization.Rd
man/replicatesCV.Rd
man/replicatesSpearmancor.Rd
man/rms.Rd
man/rnaither.Rd
man/saveDataset.Rd
man/saveOldIntensityColumns.Rd
man/savepValVec.Rd
man/scoredDataset1.Rd
man/scoredDataset2.Rd
man/spatialDistrib.Rd
man/spatialDistribHits.Rd
man/subtractBackground.Rd
man/sumChannels.Rd
man/summarizeReps.Rd
man/summarizeRepsNoFiltering.Rd
man/trim.Rd
man/varAdjust.Rd
man/vennDiag.Rd
man/volcanoPlot.Rd
vignettes
vignettes/Control_density_(1).png
vignettes/QQ_plot_(1).png
vignettes/Spatial_I_distribution_(1)_Exp_1_Plate_1_.png
vignettes/Spatial_hits_distribution_(ZScore)_Exp_1_Plate_1_.png
vignettes/hits_table.png
vignettes/norm_Spatial_I_distribution_(1)_(1)_Exp_1_Plate_1_.png
vignettes/vignetteRNAither.Rnw
vignettes/workflow.png
RNAither documentation built on May 20, 2017, 9:25 p.m.