RNAinteract: Estimate Pairwise Interactions from multidimensional features

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RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.

Author
Bernd Fischer <b.fischer@dkfz.de>
Date of publication
None
Maintainer
Bernd Fischer <b.fischer@dkfz.de>
License
Artistic-2.0
Version
1.22.0

View on Bioconductor

Man pages

bindsamples
bind RNAinteract objects along screens
computePI
compute pairwise interaction
computePValues
compute p-values
createCellHTSFromFiles
create cellHTS2 object from text files
createRNAinteract
create a RNAinteract object
createRNAinteractFromFiles
create an RNAinteract object from text files
embedPCA
Computes a PCA for a pairwise interaction matrix.
estimateMainEffect
estimate main effect
getData
Primary access function for all screen data.
getMain
get main effects
getReplicateData
Extract replicates measurements from the screen.
getSampleNames
get names of screens and channels
getScale
get scale information for a channel.
grid.doublePerturbation
Double Perturbation Plot Grob
grid.sgiHeatmap
A heatmap grob
normalizeMainEffectQuery
normalize query main effect
normalizeMainEffectTemplate
normalize template main effect
normalizePlateEffect
Normalization of plate effects
plotDoublePerturbation
Double Perturbation Plot
plotHeatmap
plots a heatmap for an interaction screen.
reportAnnotation
Specialized report functions
RNAinteract-class
Class "RNAinteract"
RNAinteract-package
Analysis of Pairwise Interaction Screens.
sgi
Dataset of class 'RNAinteract'
sgisubset
subset of an RNAinteract object.
sgisubsetQueryDesign
Subsetting query genes in a RNAinteract object.
startReport
start and end a RNAinteract report
summarizeSamples
summarize screens
swaptree
Swaps a branch of a hclust object.

Files in this package

RNAinteract/DESCRIPTION
RNAinteract/NAMESPACE
RNAinteract/R
RNAinteract/R/AllClass.R
RNAinteract/R/computePvalue.R
RNAinteract/R/createCellHTS.R
RNAinteract/R/createRNAinteract.R
RNAinteract/R/dataAccess.R
RNAinteract/R/grid.doublePerturbation.R
RNAinteract/R/grid.sgiHeatmap.R
RNAinteract/R/mainEffects.R
RNAinteract/R/normalization.R
RNAinteract/R/plotDoublePerturbation.R
RNAinteract/R/plotHeatmap.R
RNAinteract/R/report.R
RNAinteract/R/reportAnnotation.R
RNAinteract/R/reportDoublePerturbation.R
RNAinteract/R/reportGeneLists.R
RNAinteract/R/reportHeatmap.R
RNAinteract/R/reportMainEffects.R
RNAinteract/R/reportNetworks.R
RNAinteract/R/reportPCA.R
RNAinteract/R/reportScreenSGI.R
RNAinteract/R/reportStatistics.R
RNAinteract/R/subsetting.R
RNAinteract/R/transformation.R
RNAinteract/build
RNAinteract/build/vignette.rds
RNAinteract/data
RNAinteract/data/sgi.rda
RNAinteract/inst
RNAinteract/inst/CITATION
RNAinteract/inst/RNAinteractExample
RNAinteract/inst/RNAinteractExample/DataRNAinteractExample_1.txt
RNAinteract/inst/RNAinteractExample/DataRNAinteractExample_2.txt
RNAinteract/inst/RNAinteractExample/Platelist.txt
RNAinteract/inst/RNAinteractExample/QueryDesign.txt
RNAinteract/inst/RNAinteractExample/Reagents.txt
RNAinteract/inst/RNAinteractExample/Targets.txt
RNAinteract/inst/RNAinteractExample/TemplateDesign.txt
RNAinteract/inst/RNAinteractExample/networks.txt
RNAinteract/inst/doc
RNAinteract/inst/doc/RNAinteract.R
RNAinteract/inst/doc/RNAinteract.Rnw
RNAinteract/inst/doc/RNAinteract.pdf
RNAinteract/inst/makeExample
RNAinteract/inst/makeExample/makeExample.Rnw
RNAinteract/man
RNAinteract/man/RNAinteract-class.Rd
RNAinteract/man/RNAinteract-package.Rd
RNAinteract/man/bindsamples.Rd
RNAinteract/man/computePI.Rd
RNAinteract/man/computePValues.Rd
RNAinteract/man/createCellHTSFromFiles.Rd
RNAinteract/man/createRNAinteract.Rd
RNAinteract/man/createRNAinteractFromFiles.Rd
RNAinteract/man/embedPCA.Rd
RNAinteract/man/estimateMainEffect.Rd
RNAinteract/man/getData.Rd
RNAinteract/man/getMain.Rd
RNAinteract/man/getReplicateData.Rd
RNAinteract/man/getSampleNames.Rd
RNAinteract/man/getScale.Rd
RNAinteract/man/grid.doublePerturbation.Rd
RNAinteract/man/grid.sgiHeatmap.Rd
RNAinteract/man/normalizeMainEffectQuery.Rd
RNAinteract/man/normalizeMainEffectTemplate.Rd
RNAinteract/man/normalizePlateEffect.Rd
RNAinteract/man/plotDoublePerturbation.Rd
RNAinteract/man/plotHeatmap.Rd
RNAinteract/man/reportAnnotation.Rd
RNAinteract/man/sgi.Rd
RNAinteract/man/sgisubset.Rd
RNAinteract/man/sgisubsetQueryDesign.Rd
RNAinteract/man/startReport.Rd
RNAinteract/man/summarizeSamples.Rd
RNAinteract/man/swaptree.Rd
RNAinteract/vignettes
RNAinteract/vignettes/RNAinteract.Rnw