Files in GabrielHoffman/variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments
.Rbuildignore
.gitignore
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
docs/404.html
docs/articles/FAQ.html
docs/articles/additional_visualization.html
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docs/articles/additional_visualization_files/figure-html/corStructf-1.png
docs/articles/dream.html
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docs/articles/errors.html
docs/articles/index.html
docs/articles/mvtests.html
docs/articles/rnd_effects.html
docs/articles/variancePartition.html
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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
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man/BIC.MArrayLM2.Rd
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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
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man/fitVarPartModel-method.Rd
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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
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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
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tests/runTests.R
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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
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vignettes/library.bib
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vignettes/rnd_effects.Rmd
vignettes/variancePartition.Rmd
vignettes/variancePartition.tex
