• 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 2 Power Analyses

Resources:

https://medium.com/brown-compbiocore/power-analyses-for-microbiome-studies-with-micropower-8ff28b36dfe3

https://gist.github.com/brendankelly/6673e8596d3cde3fac7d493d7747aa80

http://joey711.github.io/waste-not-supplemental/simulation-cluster-accuracy/simulation-cluster-accuracy-server.html