Microbiome Analysis

  1. Diversity Analysis Methods
    1. Alpha Diversity Assessment
      1. Richness Measures
        1. Observed Species Count
          1. Chao1 Estimator
            1. ACE Estimator
              1. Jackknife Estimators
              2. Evenness Measures
                1. Pielou's Evenness
                  1. Simpson's Evenness
                    1. Camargo's Evenness
                    2. Combined Diversity Indices
                      1. Shannon Diversity Index
                        1. Simpson Diversity Index
                          1. Fisher's Alpha
                            1. Berger-Parker Index
                            2. Rarefaction Analysis
                              1. Rarefaction Curves
                                1. Sample Size Standardization
                                  1. Extrapolation Methods
                                2. Beta Diversity Analysis
                                  1. Distance Metric Selection
                                    1. Presence-Absence Metrics
                                      1. Jaccard Distance
                                        1. Sorensen Distance
                                          1. Binary Euclidean
                                          2. Abundance-Based Metrics
                                            1. Bray-Curtis Dissimilarity
                                              1. Euclidean Distance
                                                1. Manhattan Distance
                                                2. Phylogenetic Metrics
                                                  1. UniFrac Distance
                                                    1. Weighted UniFrac
                                                      1. Generalized UniFrac
                                                    2. Ordination Methods
                                                      1. Principal Coordinates Analysis
                                                        1. Non-Metric Multidimensional Scaling
                                                          1. Principal Component Analysis
                                                            1. Correspondence Analysis
                                                            2. Visualization Techniques
                                                              1. Ordination Plots
                                                                1. Heatmaps
                                                                  1. Hierarchical Clustering
                                                                    1. Network Analysis
                                                                  2. Phylogenetic Diversity Analysis
                                                                    1. Phylogenetic Tree Construction
                                                                      1. Multiple Sequence Alignment
                                                                        1. Tree Building Methods
                                                                          1. Tree Validation
                                                                          2. Phylogenetic Diversity Metrics
                                                                            1. Faith's Phylogenetic Diversity
                                                                              1. Mean Pairwise Distance
                                                                                1. Nearest Taxon Index
                                                                                2. Community Phylogenetics
                                                                                  1. Phylogenetic Signal
                                                                                    1. Community Assembly Patterns
                                                                                      1. Null Model Testing

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                                                                                  7. Taxonomic Analysis and Profiling

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                                                                                  9. Functional Analysis Approaches