Microbiome Analysis

  1. Statistical Analysis and Hypothesis Testing
    1. Data Preprocessing and Normalization
      1. Count Data Characteristics
        1. Compositional Nature
          1. Zero Inflation
            1. Overdispersion
            2. Normalization Strategies
              1. Rarefaction
                1. Relative Abundance
                  1. Total Sum Scaling
                    1. Centered Log-Ratio Transformation
                      1. Variance Stabilizing Transformation
                      2. Data Transformation Methods
                        1. Log Transformation
                          1. Square Root Transformation
                            1. Hellinger Transformation
                              1. Arcsine Transformation
                            2. Diversity Statistical Testing
                              1. Alpha Diversity Comparisons
                                1. Parametric Tests
                                  1. Non-Parametric Tests
                                    1. Multiple Comparison Correction
                                      1. Effect Size Calculation
                                      2. Beta Diversity Testing
                                        1. PERMANOVA Analysis
                                          1. ANOSIM Testing
                                            1. Mantel Tests
                                              1. Procrustes Analysis
                                              2. Multivariate Analysis
                                                1. Canonical Correspondence Analysis
                                                  1. Redundancy Analysis
                                                    1. Distance-Based RDA
                                                  2. Differential Abundance Analysis
                                                    1. Statistical Models for Count Data
                                                      1. Negative Binomial Models
                                                        1. Zero-Inflated Models
                                                          1. Hurdle Models
                                                          2. Compositional Data Analysis
                                                            1. DESeq2 Analysis
                                                              1. edgeR Analysis
                                                                1. ANCOM-BC Testing
                                                                  1. ALDEx2 Analysis
                                                                  2. Multiple Testing Correction
                                                                    1. False Discovery Rate
                                                                      1. Bonferroni Correction
                                                                        1. Benjamini-Hochberg Procedure
                                                                      2. Biomarker Discovery
                                                                        1. Feature Selection Methods
                                                                          1. Univariate Filtering
                                                                            1. Recursive Feature Elimination
                                                                              1. LASSO Regularization
                                                                              2. Machine Learning Approaches
                                                                                1. Random Forest Classification
                                                                                  1. Support Vector Machines
                                                                                    1. Gradient Boosting
                                                                                      1. Neural Networks
                                                                                      2. Validation Strategies
                                                                                        1. Cross-Validation
                                                                                          1. Independent Test Sets
                                                                                            1. Bootstrap Validation
                                                                                            2. Biomarker Evaluation
                                                                                              1. ROC Curve Analysis
                                                                                                1. Precision-Recall Curves
                                                                                                  1. Performance Metrics
                                                                                                2. Association and Correlation Analysis
                                                                                                  1. Correlation Methods
                                                                                                    1. Pearson Correlation
                                                                                                      1. Spearman Correlation
                                                                                                        1. Kendall's Tau
                                                                                                        2. Network Analysis
                                                                                                          1. Co-Occurrence Networks
                                                                                                            1. Correlation Networks
                                                                                                              1. Network Topology
                                                                                                                1. Community Detection
                                                                                                                2. Environmental Association
                                                                                                                  1. Canonical Correlation Analysis
                                                                                                                    1. Multivariate Regression
                                                                                                                      1. Environmental Fitting

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                                                                                                                  9. Functional Analysis Approaches

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                                                                                                                  11. Advanced Analytical Approaches