RNAinteract: Estimate Pairwise Interactions from multidimensional features

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.

AuthorBernd Fischer <b.fischer@dkfz.de>
Date of publicationNone
MaintainerBernd Fischer <b.fischer@dkfz.de>
LicenseArtistic-2.0
Version1.22.0

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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

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