Pointers to statistical analysis of Microbiome Data (in R)

Susan Holmes

2017-07-27

Goals for these slides: only pointers

Phyloseq

Phyloseq API

Phyloseq API

Heterogeneous Data Objects: S4 classes

(McMurdie and Holmes, 2013, Plos ONE).

phyloseq-measures-ggplot2

phyloseq-measures-ggplot2

phyloseq-ordinations All standard ordinations.

Variance stabilizing using DESeq2

VST Wolfgang Huber

The way the authors proceed is to follow the rarefying path, this is not recommended and a much better procedure is to use DESeq with phyloseq, see the wiki here:

DESeq with phyloseq wiki

phyloseq-testing-deseq

phyloseq-testing-deseq

Waste Not want not supplement

Hierarchical testing (Kris Sankaran)

Using the tree

Using the tree

In the Workflow

Taking account of the phylogenetic tree when testing:

Multiple table analyses

Sparse Canonical Correlation Analysis:

Triplot

Triplot

In the Workflow

Modulated DPCoA

DPCoA start with taxa

DPCoA start with taxa

CRAN package (with shiny adaptation): adaptiveGPCA

Multiple choices: example of the Enterotypes data:

Nature Paper Reproducible Research

Longitudinal Data Analyses

Perturbation Design

Perturbation Design

Vaginal Microbiome and Pregnancy

Markov Model

Markov Model

All Rmd and htmls for PNAS

Looking at longitudinal data in the presence of a tree using treelapse.

Example Sankey

Example Sankey

Howto Sankey

Example Treebox (Kris Sankaran)

Example Treebox (Kris Sankaran)

Tutorial to follow (Kris Sankaran)

References

Workflow paper

Workflow html

Reproducible Research links