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.clr-method | Compute an 'aldex.clr' Object |
aldex.clr.function | Compute an 'aldex.clr' Object |
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.kw | Calculate the Kruskal-Wallis test and glm ANOVA statistics |
aldex.plot | Plot an 'aldex' Object |
aldex.plotFeature | Generate dispersion, difference, and effect density plots for a feature, given an 'aldex' Object |
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 |
ALDEx2m | Analysis of differential abundance taking sample variation into account |
getDenom | getDenom |
getDenom-method | getDenom |
getFeatureNames | getFeatureNames |
getFeatureNames-method | getFeatureNames |
getFeatures | getFeatures |
getFeatures-method | getFeatures |
getMonteCarloInstances | getMonteCarloInstances |
getMonteCarloInstances-method | getMonteCarloInstances |
getMonteCarloReplicate | getMonteCarloReplicate |
getMonteCarloReplicate-method | getMonteCarloReplicate |
getMonteCarloSample | getMonteCarloSample |
getMonteCarloSample-method | getMonteCarloSample |
getReads | getReads |
getReads-method | getReads |
getSampleIDs | getSampleIDs |
getSampleIDs-method | getSampleIDs |
numConditions | numConditions |
numConditions-method | numConditions |
numFeatures | numFeatures |
numFeatures-method | numFeatures |
numMCInstances | numMCInstances |
numMCInstances-method | numMCInstances |
selex | Selection-based differential sequence variant abundance dataset |
synth2 | Synthetic asymmetric dataset |