forked from microbiome/course_2021_radboud
-
Notifications
You must be signed in to change notification settings - Fork 0
/
09-material.Rmd
67 lines (33 loc) · 2.43 KB
/
09-material.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
# Study material
## Lecture slides
See [slides](https://github.com/microbiome/course_2021_radboud/tree/main/slides).
## R programming resources
* R programming basics: [Base R](https://www.rstudio.com/wp-content/uploads/2016/10/r-cheat-sheet-3.pdf)
* Basics of R programming: [Base R](https://raw.githubusercontent.com/rstudio/cheatsheets/master/base-r.pdf)
* [R cheat sheets](https://www.rstudio.com/resources/cheatsheets/)
* R visualization with [ggplot2](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
* 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)
* 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)
## 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)