Contents

  1. Cover
  2. Front Matter
  3. 1. Introduction to QIIME 2
  4. 2. Introduction to R for Microbiome Data
  5. 3. Basic Data Processing in QIIME 2
  6. 4. Building Feature Table and Feature Representative Sequences from Raw Reads
  7. 5. Assigning Taxonomy, Building Phylogenetic Tree
  8. 6. Clustering Sequences into OTUs
  9. 7. OTU Methods in Numerical Taxonomy
  10. 8. Moving Beyond OTU Methods
  11. 9. Alpha Diversity
  12. 10. Beta Diversity Metrics and Ordination
  13. 11. Statistical Testing of Beta Diversity
  14. 12. Differential Abundance Analysis of Microbiome Data
  15. 13. Zero-Inflated Beta Models for Microbiome Data
  16. 14. Compositional Analysis of Microbiome Data
  17. 15. Linear Mixed-Effects Models for Longitudinal Microbiome Data
  18. 16. Introduction to Generalized Linear Mixed Models
  19. 17. Generalized Linear Mixed Models for Longitudinal Microbiome Data
  20. 18. Multivariate Longitudinal Microbiome Models
  21. Back Matter

Landmarks

  1. Cover
  2. Table of Contents
  3. Body Matter