Man pages for ggloor/ALDEx_bioc
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
| aldex | Compute an 'aldex' Object |
| ALDEx2m-package | Analysis of differential abundance taking sample variation... |
| aldex.clr-class | The aldex.clr class |
| aldex.clr.function | Compute an 'aldex.clr' Object Generate Monte Carlo samples of... |
| 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,... |
| aldex.glm | Calculate glm test statistics using a 'model.matrix' |
| aldex.glm.effect | calculate effect sizes and differences between all contrasts... |
| 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.senAnalysis | Sensitivity analysis using scale simulation |
| aldex.set.mode | identify set of denominator features for log-ratio... |
| aldex.ttest | Calculate Wilcoxon Rank Sum test and Welch's t-test... |
| getConditions-method | getConditions |
| getDenom-method | getDenom |
| getDirichletInstances-method | getDirichletInstances |
| getDirichletReplicate-method | getDirichletReplicate |
| getDirichletSample-method | getDirichletSample |
| getFeatureNames-method | getFeatureNames |
| getFeatures-method | getFeatures |
| getMonteCarloInstances-method | getMonteCarloInstances |
| getMonteCarloReplicate-method | getMonteCarloReplicate |
| getMonteCarloSample-method | getMonteCarloSample |
| getReads-method | getReads |
| getSampleIDs-method | getSampleIDs |
| getScaleSamples-method | getScaleSamples |
| interpretGamma | Interpret the scale model implied by a certain level of gamma... |
| numConditions-method | numConditions |
| numFeatures-method | numFeatures |
| numMCInstances-method | numMCInstances |
| plotGamma | Create gamma diagram for scale simulation sensitivity result |
| selex | Selection-based differential sequence variant abundance... |
| synth2 | Synthetic asymmetric dataset |
