RNAither: Statistical analysis of high-throughput RNAi screens

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

Author
Nora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Date of publication
None
Maintainer
Lars Kaderali <lars.kaderali@uni-greifswald.de>
License
Artistic-2.0
Version
2.22.0

View on Bioconductor

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)

Files in this package

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