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09-material.Rmd
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09-material.Rmd
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# Study material
## Lecture slides
See [slides](https://github.com/microbiome/course_2021_radboud/tree/main/slides).
## R programming resources
R progamming
* [Base R cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/10/r-cheat-sheet-3.pdf)
* [Base R cheat sheet 2](https://raw.githubusercontent.com/rstudio/cheatsheets/master/base-r.pdf)
* [Cheat sheet collection](https://www.rstudio.com/resources/cheatsheets/)
Visualization
* [ggplot2 cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/11/ggplot2-cheatsheet-2.1.pdf)
* [R graphics cookbook](http://www.cookbook-r.com/Graphs/)
Rmarkdown
* [Rmarkdown tips](https://rmarkdown.rstudio.com/)
RStudio
* [RStudio cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/01/rstudio-IDE-cheatsheet.pdf)
## Resources for TreeSummarizedExperiment
SummarizedExperiment
- [Publication](https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html)
- [Project page](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
TreeSummarizedExperiment
- [Publication](https://f1000research.com/articles/9-1246)
- [Project page](https://www.bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.html)
SingleCellExperiment
- [Publication](https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html)
- [Project page](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
## Resources for phyloseq
* [List of R tools for microbiome analysis](https://microsud.github.io/Tools-Microbiome-Analysis/)
* [phyloseq](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061217)
* [microbiome tutorial](http://microbiome.github.io/tutorials/)
* [microbiomeutilities](https://microsud.github.io/microbiomeutilities/)
* Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses ([Callahan et al. F1000, 2016](https://f1000research.com/articles/5-1492/v2)).
## Further reading
* [Data Analysis and Visualization in R for Ecologists](https://datacarpentry.org/R-ecology-lesson/) by Data Carpentry
* [Modern Statistics for Modern Biology. Holmes & Huber (2018)](http://web.stanford.edu/class/bios221/book/) for background in statistical analysis
* [Microbiome Data Science. Shetty & Lahti, 2019](https://openresearchlabs.github.io/publications/papers/2018-Shetty-Lahti-MDS.pdf)