ALDEx2m-package         Analysis of differential abundance taking
                        sample variation into account
aldex                   Compute an 'aldex' Object
aldex.clr               Compute an 'aldex.clr' Object
aldex.clr-class         The aldex.clr class
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 constrasts for the aldex.glm model matrix
aldex.kw                Calculate the Kruskal-Wallis test and glm ANOVA
                        statistics
aldex.plot              Plot an 'aldex' Object
aldex.plotFeature       Show dispersion of the expected values returned
                        by 'aldex.effect'
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
getDenom                getDenom
getFeatureNames         getFeatureNames
getFeatures             getFeatures
getMonteCarloInstances
                        getMonteCarloInstances
getMonteCarloReplicate
                        getMonteCarloReplicate
getMonteCarloSample     getMonteCarloSample
getReads                getReads
getSampleIDs            getSampleIDs
numConditions           numConditions
numFeatures             numFeatures
numMCInstances          numMCInstances
selex                   Selection-based differential sequence variant
                        abundance dataset
synth2                  Synthetic asymmetric dataset
