Chapter 10 Study material
10.1 Lecture slides
See slides.
10.2 R programming resources
R progamming
Visualization
Rmarkdown
RStudio
10.3 Resources for TreeSummarizedExperiment
SummarizedExperiment
TreeSummarizedExperiment
SingleCellExperiment
10.4 Resources for phyloseq
- List of R tools for microbiome analysis
- phyloseq
- microbiome tutorial
- microbiomeutilities
- Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses (Callahan et al. F1000, 2016).
10.5 Further reading
Data Analysis and Visualization in R for Ecologists by Data Carpentry
Modern Statistics for Modern Biology. Holmes & Huber (2018) for background in statistical analysis