├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── ALDEx2.Rproj ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AllClasses.R ├── AllGenerics.R ├── aldex-scaleSim.R ├── aldex.r ├── clr_corr.R ├── clr_effect.r ├── clr_function.r ├── clr_glm-tpq.R ├── clr_glm.r ├── clr_ttest.r ├── expectedDistance.aldex.r ├── glm_effect.r ├── iqlr_features.r ├── makeScaleMatrix.r ├── plot.aldex.glm.r ├── plot.aldex.r ├── plotFeature.aldex.r ├── progress.R ├── rdirichlet.r └── stats.fast.R ├── README.Rmd ├── README.md ├── data ├── .DS_Store ├── selex.txt.gz └── synth2.txt.gz ├── inst └── CITATION ├── man ├── .DS_Store ├── ALDEx2m-package.Rd ├── aldex.Rd ├── aldex.clr-class.Rd ├── aldex.clr.function.Rd ├── aldex.corr.Rd ├── aldex.effect.Rd ├── aldex.expectedDistance.Rd ├── aldex.glm.Rd ├── aldex.glm.effect.Rd ├── aldex.glm.plot.Rd ├── aldex.kw.Rd ├── aldex.makeScaleMatrix.Rd ├── aldex.plot.Rd ├── aldex.plotFeature.Rd ├── aldex.senAnalysis.Rd ├── aldex.set.mode.Rd ├── aldex.ttest.Rd ├── getConditions-method.Rd ├── getDenom-method.Rd ├── getDirichletInstances-method.Rd ├── getDirichletReplicate-method.Rd ├── getDirichletSample-method.Rd ├── getFeatureNames-method.Rd ├── getFeatures-method.Rd ├── getMonteCarloInstances-method.Rd ├── getMonteCarloReplicate-method.Rd ├── getMonteCarloSample-method.Rd ├── getReads-method.Rd ├── getSampleIDs-method.Rd ├── getScaleSamples-method.Rd ├── interpretGamma.Rd ├── numConditions-method.Rd ├── numFeatures-method.Rd ├── numMCInstances-method.Rd ├── plotGamma.Rd ├── selex.Rd └── synth2.Rd ├── tests ├── .DS_Store ├── testthat.R └── testthat │ ├── test-aldex.glm.v.ttest.R │ ├── test-aldex.kw.R │ ├── test-aldex.ttest.R │ ├── test-clr-conds.R │ ├── test-scaleSim.R │ └── test-stats.fast.R └── vignettes ├── .DS_Store ├── ALDEx2_vignette.Rmd ├── ALDEx2_vignette.html ├── aldex.bib ├── main-figure-final-vertical.pdf ├── main-figure-final-vertical.png ├── scaleSim_vignette.Rmd └── scaleSim_vignette.html /.DS_Store: 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