1. Introduction | 2. Installation | 3. Run ANCOM-BC2 on a simulated dataset | 3.1 Generate simulated data | 3.2 Run ancombc2 function | 3.3 Power and FDR | 3.4 Sensitivity analysis with conservative = FALSE | 4. Benchmark the performance of ANCOM-BC2 on a null dataset | 4.1 Import example data | 4.2 Permute the bmi label | 4.3 Run ancombc2 function | 4.4 Visualization | 5. Run ANCOM-BC2 on a real cross-sectional dataset | 5.1 Import example data | 5.2 Run ancombc2 function using the phyloseq object | 5.3 Structural zeros (taxon presence/absence) | 5.4 ANCOM-BC2 primary analysis | Results for age | Results for bmi | 5.5 ANCOM-BC2 global test | 5.6 ANCOM-BC2 multiple pairwise comparisons | 5.7 ANCOM-BC2 multiple pairwise comparisons against a pre-specified group (Dunnett's type of test) | 5.8 ANCOM-BC2 pattern analysis | 5.9 Run ancombc2 function using the tse object | 5.10 Run ancombc2 function by directly providing the abundance and metadata | 6. Run ANCOM-BC2 on a real longitudinal dataset | 6.1 Import example data | 6.2 Run ancombc2 function using the phyloseq object | 6.3 ANCOM-BC2 primary analysis | 6.4 ANCOM-BC2 global test | 6.5 ANCOM-BC2 multiple pairwise comparisons | 6.6 ANCOM-BC2 Dunnett's type of test | 6.7 ANCOM-BC2 pattern analysis | 6.8 Run ancombc2 function using the tse object | 6.9 Run ancombc2 function by directly providing the abundance and metadata | 7. Bias-corrected log abundances | Session information | References

1. Introduction | 2. Installation | 3. Examples | 3.1 Import a phyloseq object | 3.2 Import a tse object | 3.3 Import a matrix or data.frame | Session information | References

1. Introduction | 2. Installation | 3. Example Data | 4. Run SECOM on a Single Ecosystem | 4.1 Run secom functions using the phyloseq object | 4.2 Visualizations | Pearson correlation with thresholding | Pearson correlation with p-value filtering | Distance correlation with p-value filtering | 4.3 Run secom functions using the tse object | 4.4 Run secom functions by directly providing the abundance and metadata | 5. Run SECOM on Multiple Ecosystems | 5.1 Data manipulation | 5.2 Run secom functions using the phyloseq object | 5.3 Visualizations | 5.4 Run secom functions using the tse object | 5.5 Run secom functions by directly providing the abundance and metadata | Session information | References

1. Introduction | 2. Installation | 3. Run ANCOM on a real cross-sectional dataset | 3.1 Import example data | 3.2 Run ancom function using phyloseq data | 3.3 Scatter plot for W statistics | 3.4 Run ancom function using tse data | 3.5 Run ancom function by directly providing the abundance and metadata | 4. Run ANCOM on a real longitudinal dataset | 4.1 Import example data | 4.2 Run ancom function using phyloseq data | 4.3 Visualization for W statistics | 4.4 Run ancom function using tse data | 4.5 Run ancom function by directly providing the abundance and metadata | Session information | References

1. Introduction | 2. Installation | 3. Example Data | 4 ANCOM-BC Implementation | 4.1 Run ancombc function using the phyloseq object | 4.2 ANCOMBC primary result | LFC | SE | Test statistic | P-values | Adjusted p-values | Differentially abundant taxa | Bias-corrected abundances | Visualization for age | Visualization for BMI | 4.3 ANCOMBC global test result | Test statistics | Visualization | 4.4 Run ancombc function using the tse object | 4.5 Run ancombc function by directly providing the abundance and metadata | Session information | References