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RNAither (version 2.20.0)

Statistical analysis of high-throughput RNAi screens

Description

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

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Version

Version

2.20.0

License

Artistic-2.0

Maintainer

Lars Kaderali

Last Published

February 15th, 2017

Functions in RNAither (2.20.0)

Plot signal channels against each other

ZScorePerScreen

ZScore normalization per experiment

headerDrosophila

the header of the genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.

compareReplicateSD

Plot the standard deviation of replicates

Computing the dynamic range

Find all replicates of a certain siRNA/gene in a dataset

Remove wells from the analysis

ZScore normalization

ZPRIMEQualControl

Computing the Z' factor

Computing the SNR

Perform a GSEA analysis of a list of genes

numCellQualControl

Quality control of the number of cells

Compute the replicate root mean square

Saving the indexes of a subset in the main dataset

joinDatasetFiles

Join dataset files

replicatesSpearmancor

Compute the correlation coefficient betwenn replicates or experiments

Return the replicate value closest to zero

eraseDataSetColumn

Remove columns from dataset

Wrapper function for full automated analysis

generateDatasetFile

Generate Dataset File

Plot normalized intensity values per well

Plotting the control density

makeBoxplotPerScreen

Generate a boxplot of the data per experiment

plotControlHistoPerscreen

Plot a histogram of the data values and controls per experiment

Generate spatial plots of intensity values

Make a QQ plot per plate

Generate a new dataset with summarized replicates

saveOldIntensityColumns

Save old intensity value columns

compareReplicates

Compare replicate values

Plotting a Venn Diagram to compare hits

furthestFromZero

Return the replicate value furthest from zero

Remove a complete plate from the analysis

percCellQualControl

Quality control of the percentage of cells

makeBoxplotControlsPerPlate

Generate a boxplot of the data vs. the controls for each plate

Plot signal intensities per well

generateRepMatNoFilter

Generate a matrix of replicates (II)

plotControlHisto

Plot a histogram of the data values and controls

A vector of p-values after a Mann-Whitney test

plotQQperscreen

Make a QQ plot per experiment

Compute the replicate mean with trimmed values

plotHistoPerplate

Plot a histogram of the data values per plate

A dataset containing an additional column showing the p-values after a Mann-Whitney test

Summarize channels

Plot a histogram of the data values

A dataset containing an additional column showing the p-values, after a median normalization and a t-test

Li Wong rank / invariant probeset normalization

Searching for common hits between different scoring methods

controlDensityPerScreen

Plotting the control density per experiment

makeBoxplotControlsPerScreen

Generate a boxplot of the data vs. the controls for each experiment

hitselectionZscorePval

Selecting hits according to ZScores and p-values

Order a dataset

plotControlHistoPerplate

Plot a histogram of the data values and controls per plate

Perform a Mann-Whitney test

a typical example RNAi dataset

a typical header of an example RNAi dataset

hitselectionPval

Selecting hits according to p-values

Lowess normalization

generateReplicateMat

Generate a matrix of replicates

Compute the correlation of variation (CV)

plotHistoPerscreen

Plot a histogram of the data values per experiment

Making a volcano plot

Save p-values to file

quantileNormalization

Quantile normalization

summarizeRepsNoFiltering

Generate a new dataset with summarized replicates

controlDensityPerPlate

Plotting the control density per plate

datasetDrosophila

Genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.

Mean, median, ... , normalization

Normalization on controls

A vector of p-values after a median normalization and a t-test

Save the normalized dataset into a dataset text file

RNAither-package

Statistical analysis of high-throughput RNAi screens

compareReplicateSDPerScreen

Plot the standard deviation of replicates for each experiment

Perform a Student's t-test

Creating a subset of a dataset according to a certain column value

incorporatepValVec

Incorporate a vector of p-values into a dataset

makeBoxplotControls

Generate a boxplot of the data vs. the controls

makeBoxplot4PlateType

Generate a boxplot of the data per plate

Adjust p-values for multiple testing

makeBoxplotPerPlate

Generate a boxplot of the data per plate

spatialDistribHits

Plotting the spatial distribution of the hits

Variance adjustment

Plot signal intensities per well (II)

compareReplicaPlates

Compare replica plates

BScore normalization

Perform a Rank Product test

Divide channel values

hitselectionZscore

Selecting hits according to ZScores

Wrapper function for full automated analysis

subtractBackground

Background substraction