Microbiome Analysis

  1. Functional Analysis Approaches
    1. Metagenomic Functional Profiling
      1. Gene Prediction and Annotation
        1. Open Reading Frame Prediction
          1. Gene Calling Algorithms
            1. Functional Annotation Pipelines
            2. Functional Database Mapping
              1. KEGG Orthology
                1. COG Categories
                  1. eggNOG Annotations
                    1. CAZy Database
                      1. Pfam Domains
                      2. Metabolic Pathway Analysis
                        1. Pathway Reconstruction
                          1. Pathway Completeness
                            1. Metabolic Network Analysis
                            2. Functional Profiling Tools
                              1. HUMAnN Pipeline
                                1. MEGAN Analysis
                                  1. MG-RAST Platform
                                2. Metatranscriptomic Analysis
                                  1. Gene Expression Quantification
                                    1. Read Mapping to Genes
                                      1. Expression Level Calculation
                                        1. Normalization Methods
                                        2. Functional Activity Assessment
                                          1. Active vs Potential Function
                                            1. Temporal Expression Patterns
                                              1. Condition-Specific Activity
                                              2. Pathway Activity Analysis
                                                1. Active Pathway Identification
                                                  1. Pathway Expression Levels
                                                    1. Regulatory Network Analysis
                                                  2. Predictive Functional Profiling
                                                    1. Phylogenetic Inference Methods
                                                      1. PICRUSt2 Analysis
                                                        1. Tax4Fun Predictions
                                                          1. Faprotax Assignments
                                                          2. Prediction Accuracy Assessment
                                                            1. Validation Strategies
                                                              1. Limitation Understanding
                                                                1. Bias Evaluation
                                                                2. Comparative Analysis
                                                                  1. Predicted vs Observed Function
                                                                    1. Method Comparison
                                                                      1. Best Practice Guidelines

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                                                                  8. Diversity Analysis Methods

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                                                                  10. Statistical Analysis and Hypothesis Testing