Complete Microbiome Analysis
Introduction
Overview of sections
I Part 1: Samples to Sequences
1
Experimental Design Considerations
1.1
Amplicon versus Shotgun
1.2
16S Resources
2
Power Analyses
3
Sequencing samples
II Working with Sequence Data
4
Filtering and cleaning
5
Generating Abundance Tables
5.1
Dada2 notes
6
Remove Contaminants
7
Functional Annotation
7.1
Amplicon sequences
7.1.1
Picrust2 notes
7.2
Shotgun sequences
III Working with Abundance Tables
8
Alpha diversity
9
Beta Diversity
10
Differential Abundance
10.1
Corncob notes
10.2
DESeq2 notes
10.3
metagenomeSeq
11
Normalization Methods
12
Multivariate Analysis
IV Advanced Topics
13
Reproducible Workflows
13.1
Snakemake
14
Multiomic Methods
14.1
Correlation Analysis
14.2
Network Analysis
References
Published with bookdown
Complete Microbiome Analysis
Chapter 4
Filtering and cleaning