Package: RNAinteract 1.51.0

Mike Smith

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.

Authors:Bernd Fischer [aut], Wolfgang Huber [ctb], Mike Smith [cre]

RNAinteract_1.51.0.tar.gz
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RNAinteract.pdf |RNAinteract.html✨
RNAinteract/json (API)

# Install 'RNAinteract' in R:
install.packages('RNAinteract', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • sgi - Dataset of class 'RNAinteract'

On BioConductor:RNAinteract-1.53.0(bioc 3.20)RNAinteract-1.52.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

37 exports 0.91 score 103 dependencies 1 mentions

Last updated 9 months agofrom:fdf2c5cce2

Exports:bindscreenscomputePIcomputePValuescreateCellHTSFromFilescreateRNAinteractcreateRNAinteractFromFilesdoublePerturbationGrobembedPCAendReportestimateMainEffectgetChannelNamesgetDatagetIndDesignDatagetMaingetMainNeggetReplicateDatagetScalegetScreenNamesgrid.doublePerturbationgrid.sgiHeatmapnormalizeMainEffectQuerynormalizeMainEffectTemplatenormalizePlateEffectplotDoublePerturbationplotHeatmappostDrawDetails.doublePerturbationreportAnnotationreportDoublePerturbationreportGeneListsreportHeatmapreportMainEffectsreportNetworksreportScreenDatareportStatisticssgisubsetstartReportsummarizeScreens

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocManagerBiostringsbitbit64bitopsblobcachemCategorycaToolscellHTS2clicolorspacecpp11crayoncurlDBIdeldirfansifarverfastmapgenefiltergeneplotterGenomeInfoDbGenomeInfoDbDataggplot2gluegplotsgraphGSEABasegtablegtoolshttrhwriterICSICSNPinterpIRangesisobandjpegjsonliteKEGGRESTKernSmoothlabelinglatticelatticeExtralifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamitoolsmunsellmvtnormnlmenumDerivopensslpillarpkgconfigplogrpngpreprocessCoreR6RBGLRColorBrewerRcppRcppArmadilloRcppEigenrlangRSQLiteS4VectorsscalessplotsstatmodsurveysurvivalsystibbleUCSC.utilsutf8vctrsviridisLitevsnwithrXMLxtableXVectorzlibbioc

RNAinteract

Rendered fromRNAinteract.Rnwusingutils::Sweaveon May 02 2024.

Last update: 2018-08-30
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Analysis of Pairwise Interaction Screens.RNAinteract-package RNAinteract
bind RNAinteract objects along screensbindscreens
compute pairwise interactioncomputePI
compute p-valuescomputePValues
create cellHTS2 object from text filescreateCellHTSFromFiles
create a RNAinteract objectcreateRNAinteract
create an RNAinteract object from text filescreateRNAinteractFromFiles
Computes a PCA for a pairwise interaction matrix.embedPCA
estimate main effectestimateMainEffect
Primary access function for all screen data.getData
get main effectsgetMain getMainNeg
Extract replicates measurements from the screen.getIndDesignData getReplicateData
get scale information for a channel.getScale
get names of screens and channelsgetChannelNames getScreenNames
Double Perturbation Plot GrobdoublePerturbationGrob grid.doublePerturbation postDrawDetails.doublePerturbation
A heatmap grobgrid.sgiHeatmap
normalize query main effectnormalizeMainEffectQuery
normalize template main effectnormalizeMainEffectTemplate
Normalization of plate effectsnormalizePlateEffect
Double Perturbation PlotplotDoublePerturbation
plots a heatmap for an interaction screen.plotHeatmap
Specialized report functionsreportAnnotation reportDoublePerturbation reportGeneLists reportHeatmap reportMainEffects reportNetworks reportScreenData reportStatistics
Class "RNAinteract"RNAinteract-class show,RNAinteract-method
Dataset of class 'RNAinteract'sgi
subset of an RNAinteract object.sgisubset
Subsetting query genes in a RNAinteract object.sgisubsetQueryDesign
start and end a RNAinteract reportendReport startReport
summarize screenssummarizeScreens
Swaps a branch of a hclust object.swaptree