Files in variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments

README.md R/FMT.R R/ESS.R R/plotStratifyBy.R R/misc.R R/plotCorrStructure.R R/sortCols.R R/voomWithDreamWeights.R R/checkModelStatus.R R/get_prediction.R R/fitModels.R R/plotContrasts.R R/heatmap.R R/calcVarPart.R R/canCorPairs.R R/fitMixedModelDE.R R/toptable.R R/plots.R R/eBayesFMT.R R/data_annotation.R R/confidenceIntervals.R R/plotCorrMatrix.R R/extractVarPart.R vignettes/FAQ.Rmd vignettes/dream.Rmd vignettes/additional_visualization.Rmd man/colinearityScore.Rd man/varPartData.Rd man/ggColorHue.Rd man/voomWithDreamWeights.Rd man/varParFrac-class.Rd man/fitExtractVarPartModel-method.Rd man/get_prediction-method.Rd man/MArrayLM2-class.Rd man/toptable-method.Rd man/as.matrix-varPartResults-method.Rd man/eBayesFMT.Rd man/plotStratifyBy.Rd man/plotCorrStructure.Rd man/VarParFitList-class.Rd man/plotCompareP-method.Rd man/fitVarPartModel-method.Rd man/sortCols-method.Rd man/eBayes-method.Rd man/plotVarPart-method.Rd man/varPartDEdata.Rd man/residuals-MArrayLM2-method.Rd man/classifyTestsF-MArrayLM2-method.Rd man/plotCorrMatrix.Rd man/classifyTestsF.Rd man/as.data.frame-varPartResults-method.Rd man/plotPercentBars.Rd man/calcVarPart-method.Rd man/dot-isMixedModelFormula.Rd man/FMT-class.Rd man/canCorPairs.Rd man/FMT.ZI.Rd man/VarParCIList-class.Rd man/extractVarPart.Rd man/FMT.Rd man/residuals-VarParFitList-method.Rd man/dream-method.Rd man/subset.MArrayLM2-method.Rd man/dot-getAllUniContrasts.Rd man/ESS-method.Rd man/residuals-MArrayLM-method.Rd man/getContrast-method.Rd man/varPartConfInf.Rd man/dot-standard_transform.Rd man/plotStratify.Rd man/plotContrasts.Rd man/varPartResults-class.Rd tests/runTests.R inst/doc/FAQ.Rmd inst/doc/dream.Rmd inst/doc/theory_practice_random_effects.R inst/doc/additional_visualization.Rmd inst/doc/theory_practice_random_effects.pdf inst/doc/additional_visualization.R inst/doc/FAQ.R inst/doc/dream.R inst/doc/variancePartition.R inst/doc/variancePartition.pdf inst/unitTests/test_dream_bplapply.R inst/unitTests/test_voomWithDreamWeights.R inst/unitTests/test_residuals.R inst/unitTests/test_combined_contrasts.R inst/unitTests/test_sparseMatrix.R