GabrielHoffman/variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments

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GabrielHoffman/variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments
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Quantify and interpret drivers of variation in multilevel gene expression experiments

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DESCRIPTION
NAMESPACE
NEWS.md R/ESS.R R/applyQualityWeights.R R/augmentPriorCount.R R/calcVarPart.R R/canCorPairs.R R/checkModelStatus.R R/confidenceIntervals.R R/contrasts.R R/data_annotation.R R/diffVar.R R/dream.R R/extractVarPart.R R/fitExtractVarPartModel.R R/fitMixedModel.R R/fitMixedModelDE.R R/fitVarPartModel.R R/get_prediction.R R/hatvalues.R R/heatmap.R R/isRunableFormula.R R/iterator.R R/logLik.R R/misc.R R/mvTest.R R/plotContrasts.R R/plotCorrMatrix.R R/plotCorrStructure.R R/plotStratifyBy.R R/plots.R R/rdf_functions.R R/sortCols.R R/toptable.R R/treat.R R/vcov.R R/vcovSqrt.R R/voomWithDreamWeights.R README.md
TODO
_pkgdown.yml
data/varPartDEdata.rda
data/varPartData.rda
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inst/CITATION
inst/REFERENCES.bib
inst/unitTests/test_Ftests.R inst/unitTests/test_calcVarPart.R inst/unitTests/test_combined_contrasts.R inst/unitTests/test_ddf.R inst/unitTests/test_dream_bplapply.R inst/unitTests/test_hatvalues.R inst/unitTests/test_logLik.R inst/unitTests/test_residuals.R inst/unitTests/test_sparseMatrix.R inst/unitTests/test_treat.R inst/unitTests/test_vcov.R inst/unitTests/test_voomWithDreamWeights.R inst/unitTests/test_vp_dream_formulas.R man/BIC.MArrayLM.Rd man/BIC.MArrayLM2.Rd man/ESS-method.Rd man/MArrayLM2-class.Rd man/VarParCIList-class.Rd man/VarParFitList-class.Rd man/applyQualityWeights.Rd man/as.data.frame.varPartResults.Rd man/as.matrix-varPartResults-method.Rd man/augmentPriorCount.Rd man/calcVarPart-method.Rd man/canCorPairs.Rd man/classifyTestsF-MArrayLM2-method.Rd man/classifyTestsF.Rd man/colinearityScore.Rd man/deviation-method.Rd man/diffVar-method.Rd man/dot-getAllUniContrasts.Rd man/dot-isMixedModelFormula.Rd man/dot-standard_transform.Rd man/dream-method.Rd man/dscchisq.Rd man/eBayes-method.Rd man/extractVarPart.Rd
man/figures/variancePartition.png
man/fitExtractVarPartModel-method.Rd man/fitVarPartModel-method.Rd man/getContrast-method.Rd man/getTreat-method.Rd man/get_prediction-method.Rd man/ggColorHue.Rd man/hatvalues-method.Rd man/isRunableFormula.Rd man/logLik.MArrayLM.Rd man/logLik.MArrayLM2.Rd man/makeContrastsDream.Rd man/mvTest-method.Rd man/mvTest_input-class.Rd man/plotCompareP-method.Rd man/plotContrasts.Rd man/plotCorrMatrix.Rd man/plotCorrStructure.Rd man/plotPercentBars-method.Rd man/plotStratify.Rd man/plotStratifyBy.Rd man/plotVarPart-method.Rd man/plotVarianceEstimates.Rd man/rdf.Rd man/rdf.merMod.Rd man/rdf_from_matrices.Rd man/reOnly.Rd man/residuals-MArrayLM-method.Rd man/residuals-MArrayLM2-method.Rd man/residuals-VarParFitList-method.Rd man/residuals.MArrayLM2.Rd man/shrinkageMetric.Rd man/sortCols-method.Rd man/subset.MArrayLM2-method.Rd man/toptable-method.Rd man/varParFrac-class.Rd man/varPartConfInf.Rd man/varPartDEdata.Rd man/varPartData.Rd man/varPartResults-class.Rd man/vcov-MArrayLM-method.Rd man/vcov-MArrayLM2-method.Rd man/vcovSqrt-method.Rd man/voomWithDreamWeights.Rd tests/runTests.R vignettes/FAQ.Rmd vignettes/additional_visualization.Rmd vignettes/dream.Rmd vignettes/errors.Rmd vignettes/figure/DE-1.pdf vignettes/figure/DE-2.pdf vignettes/figure/IndivDominant-1.pdf vignettes/figure/IndivDominant-2.pdf vignettes/figure/IndivDominant-3.pdf vignettes/figure/IndivDominant-4.pdf vignettes/figure/IndivDominant-5.pdf vignettes/figure/IndivDominant-6.pdf vignettes/figure/canCorPairs-1.pdf vignettes/figure/plotStratify-1.pdf vignettes/figure/plotStratify-2.pdf vignettes/figure/simResult-1.pdf vignettes/figure/simResult-2.pdf vignettes/figure/siteDominant-1.pdf vignettes/figure/siteDominant-2.pdf vignettes/figure/siteDominant-3.pdf vignettes/figure/siteDominant-4.pdf vignettes/figure/siteDominant-5.pdf vignettes/figure/siteDominant-6.pdf vignettes/figure/vpInteraction-1.pdf vignettes/figure/withinTissue-1.pdf
vignettes/library.bib
vignettes/mvtests.Rmd vignettes/rnd_effects.Rmd vignettes/variancePartition.Rmd
vignettes/variancePartition.tex
GabrielHoffman/variancePartition documentation built on Nov. 8, 2024, 11:17 a.m.

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