Package: RUVcorr 1.39.0

Saskia Freytag

RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

Authors:Saskia Freytag

RUVcorr_1.39.0.tar.gz
RUVcorr_1.39.0.zip(r-4.5)RUVcorr_1.39.0.zip(r-4.4)RUVcorr_1.39.0.zip(r-4.3)
RUVcorr_1.39.0.tgz(r-4.4-any)RUVcorr_1.39.0.tgz(r-4.3-any)
RUVcorr_1.39.0.tar.gz(r-4.5-noble)RUVcorr_1.39.0.tar.gz(r-4.4-noble)
RUVcorr_1.39.0.tgz(r-4.4-emscripten)RUVcorr_1.39.0.tgz(r-4.3-emscripten)
RUVcorr.pdf |RUVcorr.html✨
RUVcorr/json (API)
NEWS

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

Peer review:

On BioConductor:RUVcorr-1.39.0(bioc 3.21)RUVcorr-1.38.0(bioc 3.20)

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

geneexpressionnormalization

3.60 score 8 scripts 217 downloads 2 mentions 24 exports 34 dependencies

Last updated 2 months agofrom:1f72b159cb. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winWARNINGNov 30 2024
R-4.5-linuxWARNINGNov 30 2024
R-4.4-winWARNINGNov 30 2024
R-4.4-macWARNINGNov 30 2024
R-4.3-winWARNINGNov 30 2024
R-4.3-macWARNINGNov 30 2024

Exports:assessQualitybackgroundcalculateThresholdcompareRankscorrelationPlotECDFPloteigenvaluePlotempNegativeControlsfindWeightsgenePlothistogramPlotis.optimizeParametersis.simulateGEdatais.Thresholdis.WeightsoptimizeParametersPCAPlotplotDesignplotThresholdprioritiseRLEPlotRUVNaiveRidgesimulateGEdatawcor

Dependencies:BHBiobaseBiocGenericsBiocParallelbladderbatchclicodetoolscorrplotcpp11formatRfutile.loggerfutile.optionsgenericsglueGPArotationgridExtragtablelambda.rlatticelifecyclemagrittrMASSmnormtnlmeplyrpsychRcppreshape2rlangsnowsnowfallstringistringrvctrs

Simulating and cleaning gene expression data using RUVcorr in the context of inferring gene co-expression

Rendered fromVignette.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2020-04-07
Started: 2020-04-07

Readme and manuals

Help Manual

Help pageTopics
Quality assessment for cleaning procedures.assessQuality
Randomly choose background genes.background
Calculates the correlation threshold.calculateThreshold
Compare ranking of known reference gene pairs.compareRanks
Correlation plot to compare estimated correlations with true correlations.correlationPlot
Plot empirical cumulative distribution function for correlations.ECDFPlot
Plot eigenvalues of SVD of the negtaive controls.eigenvaluePlot
Empirically choose negative control genes.empNegativeControls empNegativeControls.default empNegativeControls.simulateGEdata
Finds weights of each level of a factor.findWeights
Plot of means and inter-quantile ranges of all genes.genePlot
Plot histogram of correlations.histogramPlot
Checking 'optimizeParameters' class.is.optimizeParameters
Checking 'simulateGEdata' class.is.simulateGEdata
Checking 'Threshold' class.is.Threshold
Checking 'Weights' class.is.Weights
Optimize parameters of removal of unwanted variation.optimizeParameters
Plot principle component analysis for gene expression data.PCAPlot
Plots an object of class 'optimizeParameters'.plot.optimizeParameters
Plot nested design structure.plotDesign
Plots an object of class 'Threshold'.plotThreshold
Print an object of class 'simualteGEdata'.print.simulateGEdata
Prioritising candidate genes.prioritise
Plots different versions of relative log expression plotsRLEPlot
Removal of unwanted variation for gene-gene correlations.RUVcorr
Removal of unwanted variation for gene correlations.RUVNaiveRidge RUVNaiveRidge.default RUVNaiveRidge.simulateGEdata
Simulate gene expression data.simulateGEdata
Calculate weighted correlations.wcor