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

View on Bioconductor

Functions

bindscreens Man page
computePI Man page
computePValues Man page
createCellHTSFromFiles Man page
createRNAinteract Man page
createRNAinteractFromFiles Man page
doublePerturbationGrob Man page
embedPCA Man page
endReport Man page
estimateMainEffect Man page
getChannelNames Man page
getData Man page
getIndDesignData Man page
getMain Man page
getMainNeg Man page
getReplicateData Man page
getScale Man page
getScreenNames Man page
grid.doublePerturbation Man page
grid.sgiHeatmap Man page
normalizeMainEffectQuery Man page
normalizeMainEffectTemplate Man page
normalizePlateEffect Man page
plotDoublePerturbation Man page
plotHeatmap Man page
postDrawDetails.doublePerturbation Man page
reportAnnotation Man page
reportDoublePerturbation Man page
reportGeneLists Man page
reportHeatmap Man page
reportMainEffects Man page
reportNetworks Man page
reportScreenData Man page
reportStatistics Man page
RNAinteract Man page
RNAinteract-class Man page
RNAinteract-package Man page
sgi Man page
sgisubset Man page
sgisubsetQueryDesign Man page
show,RNAinteract-method Man page
startReport Man page
summarizeScreens Man page
swaptree Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.