ALDEx2m-package         Analysis of differential abundance taking
                        sample variation into account
aldex                   Compute an 'aldex' Object
aldex.clr-class         The aldex.clr class
aldex.clr.function      Compute an 'aldex.clr' Object Generate Monte
                        Carlo samples of the Dirichlet distribution for
                        each sample. Convert each instance using a
                        centered log-ratio transform. This is the input
                        for all further analyses.
aldex.corr              Calculate correlation with a continuous
                        variable
aldex.effect            Calculate effect sizes and differences between
                        conditions
aldex.expectedDistance
                        Calculate the expected values of distances
                        between samples, given an 'aldex' Object
aldex.glm               Calculate glm test statistics using a
                        'model.matrix'
aldex.glm.effect        calculate effect sizes and differences between
                        all contrasts for the aldex.glm model matrix
aldex.glm.plot          Plot an 'aldex' Object
aldex.kw                Calculate the Kruskal-Wallis test and glm
                        statistics
aldex.makeScaleMatrix   Generate a differential scale matrix by group
aldex.plot              Plot an 'aldex' Object
aldex.plotFeature       Show dispersion of the expected values returned
                        by 'aldex.effect'
aldex.senAnalysis       Sensitivity analysis using scale simulation
aldex.set.mode          identify set of denominator features for
                        log-ratio calculation
aldex.ttest             Calculate Wilcoxon Rank Sum test and Welch's
                        t-test statistics
getConditions           getConditions
getDenom                getDenom
getDirichletInstances   getDirichletInstances
getDirichletReplicate   getDirichletReplicate
getDirichletSample      getDirichletSample
getFeatureNames         getFeatureNames
getFeatures             getFeatures
getMonteCarloInstances
                        getMonteCarloInstances
getMonteCarloReplicate
                        getMonteCarloReplicate
getMonteCarloSample     getMonteCarloSample
getReads                getReads
getSampleIDs            getSampleIDs
getScaleSamples         getScaleSamples
interpretGamma          Interpret the scale model implied by a certain
                        level of gamma or scale model
numConditions           numConditions
numFeatures             numFeatures
numMCInstances          numMCInstances
plotGamma               Create gamma diagram for scale simulation
                        sensitivity result
selex                   Selection-based differential sequence variant
                        abundance dataset
synth2                  Synthetic asymmetric dataset
