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

• Rmarkdown tips

RStudio

• RStudio cheat sheet

10.3 Resources for TreeSummarizedExperiment

• SingleCellExperiment
  • Publication
  • Project page
• SummarizedExperiment
  • Publication
  • Project page
• TreeSummarizedExperiment
  • Publication
  • Project page

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

• Microbiome Data Science. Shetty & Lahti, 2019

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