RNAither: Statistical analysis of high-throughput RNAi screens

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

AuthorNora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
Date of publicationNone
MaintainerLars Kaderali <lars.kaderali@uni-greifswald.de>
LicenseArtistic-2.0
Version2.22.0

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)

Functions

BScore Man page
channelPlot Man page
closestToZero Man page
compareHits Man page
compareReplicaPlates Man page
compareReplicates Man page
compareReplicateSD Man page
compareReplicateSDPerScreen Man page
controlDensity Man page
controlDensityPerPlate Man page
controlDensityPerScreen Man page
controlNorm Man page
createSubset Man page
dataset Man page
datasetDrosophila Man page
discardLabtek Man page
discardWells Man page
divideChannels Man page
divNorm Man page
DRQualControl Man page
eraseDataSetColumn Man page
findReplicates Man page
furthestFromZero Man page
generateDatasetFile Man page
generateReplicateMat Man page
generateRepMatNoFilter Man page
gseaAnalysis Man page
header Man page
headerDrosophila Man page
hitselectionPval Man page
hitselectionZscore Man page
hitselectionZscorePval Man page
incorporatepValVec Man page
indexSubset Man page
joinDatasetFiles Man page
joinDatasets Man page
LiWongRank Man page
lowessNorm Man page
mainAnalysis Man page
makeBoxplot4PlateType Man page
makeBoxplotControls Man page
makeBoxplotControlsPerPlate Man page
makeBoxplotControlsPerScreen Man page
makeBoxplotPerPlate Man page
makeBoxplotPerScreen Man page
MannWhitney Man page
multTestAdjust Man page
numCellQualControl Man page
orderGeneIDs Man page
percCellQualControl Man page
plotBar Man page
plotControlHisto Man page
plotControlHistoPerplate Man page
plotControlHistoPerscreen Man page
plotHisto Man page
plotHistoPerplate Man page
plotHistoPerscreen Man page
plotQQ Man page
plotQQperplate Man page
plotQQperscreen Man page
pValVec1 Man page
pValVec2 Man page
quantileNormalization Man page
RankProduct Man page
replicatesCV Man page
replicatesSpearmancor Man page
rms Man page
rnaither Man page
RNAither Man page
RNAither-package Man page
saveDataset Man page
saveOldIntensityColumns Man page
savepValVec Man page
scoredDataset1 Man page
scoredDataset2 Man page
SNRQualControl Man page
spatialDistrib Man page
spatialDistribHits Man page
subtractBackground Man page
sumChannels Man page
summarizeReps Man page
summarizeRepsNoFiltering Man page
trim Man page
Ttest Man page
varAdjust Man page
vennDiag Man page
volcanoPlot Man page
ZPRIMEQualControl Man page
ZScore Man page
ZScorePerScreen Man page
ZScorePlot Man page
ZScorePlotTwo Man page

Files

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

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