Intro
Preface
Acknowledgments
Contents
About the Authors
Chapter 1: Introduction to QIIME 2
1.1 Overview of QIIME 2
1.2 Core Concepts in QIIME 2
1.2.1 Artifacts
1.2.2 Visualizations
1.2.3 Semantic Type
1.2.4 Plugins
1.3 Install QIIME 2
1.4 Store and Track Data
1.5 Extract Data from QIIME 2 Archives
1.6 Summary
References
Chapter 2: Introduction to R for Microbiome Data
2.1 Some Useful R Functions
2.1.1 Save Data into R Data Format
2.1.1.1 Use SaveRDS() to Save Single R Object
2.1.1.2 Use Save() to Save Multiple R Objects

2.1.1.3 Use Save.Image() to Save Workspace Image
2.1.2 Read Back Data from R Data Format Files
2.1.2.1 Use ReadRDS() to Read Back Single R Object
2.1.2.2 Use Load() to Read Back Multiple Objects from R File
2.1.3 Use Download.File() to Download File from Website
2.2 Some Useful R Packages for Microbiome Data
2.2.1 Readr
2.2.2 Ggpubr
2.2.2.1 Box Plots
2.2.2.2 Violin Plots
2.2.2.3 Density Plots
2.2.2.4 Histogram Plots
2.2.3 Tidyverse
2.3 Specifically Designed R Packages for Microbiome Data
2.3.1 Phyloseq
2.3.1.1 Create a phyloseq Object

2.3.1.2 Merge Samples in a phyloseq Object
2.3.1.3 Merge Two phyloseq Objects
2.3.2 Microbiome
2.3.2.1 Create a phyloseq Object
2.3.2.2 Summarize the Contents of phyloseq Object
2.3.2.3 Retrieve the Data Elements of phyloseq Object
2.3.2.4 Operate on Taxa
2.3.2.5 Aggregate Taxa to Higher Taxonomic Levels
2.3.2.6 Operate on Sample
2.3.2.7 Operate on Metadata
2.3.2.8 Data Transformations
2.3.2.9 Export phyloseq Data into CSV Files
2.3.2.10 Import CSV, Mothur, and BIOM Format Files into a phyloseq Object
2.3.3 ampvis2
2.3.4 curatedMetagenomicData

2.4 Some R Packages for Analysis of Phylogenetics
2.4.1 Ape
2.4.2 Phytools
2.4.3 Castor
2.5 BIOM Format and Biomformat Package
2.6 Creating Analysis Microbiome Dataset
2.7 Summary
References
Chapter 3: Basic Data Processing in QIIME 2
3.1 Importing Data into QIIME 2
3.1.1 Import FASTA Format Data
3.1.2 Import FASTQ Format Data
3.1.3 Import Feature Table
3.1.4 Import Phylogenetic Trees
3.2 Exporting Data from QIIME 2
3.2.1 Export Feature Table
3.2.2 Export Phylogenetic Trees
3.3 Extracting Data from QIIME 2 Archives

3.3.1 Extract Data Using the Qiime Tools Export Command
3.3.2 Extract Data Using Unzip Program on macOS
3.4 Filtering Data in QIIME 2
3.4.1 Filter Feature Table
3.4.1.1 Total-Frequency-Based Filtering
3.4.1.2 Contingency-Based Filtering
3.4.1.3 Identifier-Based Filtering
3.4.1.4 Metadata-Based Filtering
3.4.2 Taxonomy-Based Tables and Sequences Filtering
3.4.2.1 Filter Tables Based on Taxonomy
3.4.2.2 Filter Sequences Based on Taxonomy
3.4.3 Filter Distance Matrices
3.4.3.1 Filtering Distance Matrix Based on Identifiers