Microbiome Analysis

  1. Advanced Analytical Approaches
    1. Metagenome-Assembled Genomes
      1. Metagenomic Assembly
        1. Assembly Algorithms
          1. Assembly Quality Assessment
            1. Scaffolding Methods
            2. Genome Binning
              1. Composition-Based Binning
                1. Coverage-Based Binning
                  1. Hybrid Binning Approaches
                  2. MAG Quality Assessment
                    1. Completeness Estimation
                      1. Contamination Detection
                        1. Quality Metrics
                        2. MAG Annotation and Analysis
                          1. Gene Prediction
                            1. Functional Annotation
                              1. Phylogenetic Placement
                                1. Comparative Genomics
                              2. Strain-Level Analysis
                                1. Single Nucleotide Variant Detection
                                  1. Variant Calling Pipelines
                                    1. Quality Filtering
                                      1. Population Genetics
                                      2. Pangenome Analysis
                                        1. Core Genome Identification
                                          1. Accessory Genome Analysis
                                            1. Gene Presence-Absence
                                            2. Strain Tracking
                                              1. Temporal Dynamics
                                                1. Transmission Analysis
                                                  1. Source Tracking
                                                2. Multi-Omics Integration
                                                  1. Data Integration Strategies
                                                    1. Early Integration
                                                      1. Intermediate Integration
                                                        1. Late Integration
                                                        2. Multi-Omics Analysis Tools
                                                          1. mixOmics Package
                                                            1. MOFA Analysis
                                                              1. Joint Dimension Reduction
                                                              2. Systems Biology Approaches
                                                                1. Network Integration
                                                                  1. Pathway Integration
                                                                    1. Regulatory Network Analysis
                                                                    2. Visualization Methods
                                                                      1. Multi-Layer Networks
                                                                        1. Integrated Heatmaps
                                                                          1. Circos Plots

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                                                                      10. Statistical Analysis and Hypothesis Testing

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                                                                      12. Microbiome Applications in Human Health