| allDA | Run many differential abundance/expression methods |
| DA.abc | ANCOM-BC |
| DA.adx | Aldex t.test and wilcox |
| DA.anova | Run 'anova' on all features from 'DAtest' results with... |
| DA.aoa | ANOVA - Multiplicative zero-correction and additive log-ratio... |
| DA.aoc | ANOVA - Multiplicative zero-correction and additive log-ratio... |
| DA.aov | ANOVA |
| DA.bay | baySeq |
| DA.drop1 | Run 'drop1' on all features from 'DAtest' results with... |
| DA.ds2 | DESeq2 with manual geometric means |
| DA.ds2x | DESeq2 |
| DA.ere | EdgeR exact test - TMM normalization |
| DA.ere2 | EdgeR exact test - RLE normalization |
| DA.erq | EdgeR quasi-likelihood - TMM normalization |
| DA.erq2 | EdgeR quasi-likelihood - RLE normalization |
| DA.fri | Friedman Rank Sum test |
| DA.kru | Kruskal-Wallis test |
| DA.lao | ANOVA |
| DA.lao2 | ANOVA |
| DA.lia | LIMMA - Multiplicative zero-correction and additive log-ratio... |
| DA.lic | LIMMA - Multiplicative zero-correction and center log-ratio... |
| DA.lim | LIMMA |
| DA.lli | LIMMA |
| DA.lli2 | LIMMA |
| DA.llm | Log linear regression |
| DA.llm2 | Log linear regression |
| DA.lma | Linear regression - Multiplicative zero-correction and... |
| DA.lmc | Linear regression - Multiplicative zero-correction and center... |
| DA.lrm | Linear regression |
| DA.lsmeans | Run 'lsmeans' on all features from 'DAtest' results with... |
| DA.ltt | Welch t-test |
| DA.ltt2 | Welch t-test |
| DA.msf | MetagenomeSeq Feature model |
| DA.mva | Mvabund |
| DA.neb | Negative binomial glm |
| DA.pea | Pearson Correlation |
| DA.per | Permutation test of user-defined test statistic |
| DA.poi | Poisson glm |
| DA.qpo | Quasi-poisson glm |
| DA.qua | Quade test |
| DA.sam | SAMSeq |
| DA.spe | Spearman's Rank Correlation |
| DA.tta | Welch t-test - Multiplicative zero-correction and additive... |
| DA.ttc | Welch t-test - Multiplicative zero-correction and center... |
| DA.ttr | Welch t-test with rank-normalization |
| DA.ttt | Welch t-test |
| DA.TukeyHSD | Run 'TukeyHSD' on all features from 'DAtest' results with... |
| DA.vli | LIMMA with 'voom' |
| DA.wil | Wilcoxon Rank Sum and Signed Rank Test |
| DA.zig | MetagenomeSeq ZIG |
| DA.znb | Zero inflated Negative Binomial glm |
| DA.zpo | Zero inflated Poisson glm |
| DA.zzz | User-defined function |
| featurePlot | Plot association between abundance of a feature and predictor |
| norm_alr | Additive log-ratio normalization |
| norm_clr | Centered log-ratio normalization |
| plot.DA | Plotting results from 'testDA' |
| plot.DAPower | Plotting results from 'powerDA' |
| powerDA | Estimating (empirical) statistical power |
| preDA | Pre-processing for DAtest |
| print.DA | Print results from 'testDA' |
| runtimeDA | Estimate runtime of 'testDA' on large datasets |
| summary.DA | Summary of results from 'testDA' |
| summary.DAPower | Summary of results from 'powerDA' |
| testDA | Comparing differential abundance/expression methods by... |
| vennDA | Plot Venn diagram from 'allDA' object |
