variancePartition: Quantify and interpret divers of variation in multilevel gene expression experiments

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Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.

Author
Gabriel E. Hoffman
Date of publication
None
Maintainer
Gabriel E. Hoffman <gabriel.hoffman@mssm.edu>
License
GPL (>= 2)
Version
1.4.1

View on Bioconductor

Man pages

as.matrix-varPartResults-method
Convert to matrix
calcVarPart-method
Compute variance statistics
canCorPairs
canCorPairs
colinearityScore
Collinearity score
ESS-method
Effective sample size
extractVarPart
Extract variance statistics
fitExtractVarPartModel-method
Fit linear (mixed) model, report variance fractions
fitVarPartModel-method
Fit linear (mixed) model
getVarianceComponents
Extract variance terms
ggColorHue
Default colors for ggplot
plotCorrMatrix
plotCorrMatrix
plotCorrStructure
plotCorrStructure
plotPercentBars
Bar plot of variance fractions
plotStratify
plotStratify
plotStratifyBy
plotStratifyBy
plotVarPart-method
Violin plot of variance fractions
residuals-VarParFitList-method
Residuals from model fit
sortCols-method
Sort variance partition statistics
varPartConfInf
Linear mixed model confidence intervals
varPartData
Simulation dataset for examples

Files in this package

variancePartition/DESCRIPTION
variancePartition/NAMESPACE
variancePartition/NEWS
variancePartition/R
variancePartition/R/ESS.R
variancePartition/R/calcVarPart.R
variancePartition/R/canCorPairs.R
variancePartition/R/checkModelStatus.R
variancePartition/R/confidenceIntervals.R
variancePartition/R/extractVarPart.R
variancePartition/R/fitModels.R
variancePartition/R/fitVarTest.R
variancePartition/R/heatmap.R
variancePartition/R/misc.R
variancePartition/R/plotCorrMatrix.R
variancePartition/R/plotCorrStructure.R
variancePartition/R/plotStratifyBy.R
variancePartition/R/plots.R
variancePartition/R/sortCols.R
variancePartition/TODO
variancePartition/build
variancePartition/build/vignette.rds
variancePartition/data
variancePartition/data/varPartData.rda
variancePartition/inst
variancePartition/inst/CITATION
variancePartition/inst/doc
variancePartition/inst/doc/additional_visualization.R
variancePartition/inst/doc/additional_visualization.Rnw
variancePartition/inst/doc/additional_visualization.pdf
variancePartition/inst/doc/variancePartition.R
variancePartition/inst/doc/variancePartition.Rnw
variancePartition/inst/doc/variancePartition.pdf
variancePartition/man
variancePartition/man/ESS-method.Rd
variancePartition/man/as.matrix-varPartResults-method.Rd
variancePartition/man/calcVarPart-method.Rd
variancePartition/man/canCorPairs.Rd
variancePartition/man/colinearityScore.Rd
variancePartition/man/extractVarPart.Rd
variancePartition/man/fitExtractVarPartModel-method.Rd
variancePartition/man/fitVarPartModel-method.Rd
variancePartition/man/getVarianceComponents.Rd
variancePartition/man/ggColorHue.Rd
variancePartition/man/plotCorrMatrix.Rd
variancePartition/man/plotCorrStructure.Rd
variancePartition/man/plotPercentBars.Rd
variancePartition/man/plotStratify.Rd
variancePartition/man/plotStratifyBy.Rd
variancePartition/man/plotVarPart-method.Rd
variancePartition/man/residuals-VarParFitList-method.Rd
variancePartition/man/sortCols-method.Rd
variancePartition/man/varPartConfInf.Rd
variancePartition/man/varPartData.Rd
variancePartition/vignettes
variancePartition/vignettes/additional_visualization.Rnw
variancePartition/vignettes/library.bib
variancePartition/vignettes/variancePartition.Rnw