Chapter 10 Study material
10.1 Lecture slides
See slides.
10.2 R programming resources
- R programming basics: Base R
- Basics of R programming: Base R
- R cheat sheets
- R visualization with ggplot2
- R graphics cookbook
Rmarkdown
RStudio
10.3 Resources for TreeSummarizedExperiment
- SingleCellExperiment
- SummarizedExperiment
- TreeSummarizedExperiment
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
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