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polishing extra material
antagomir Jul 8, 2021
d1e009b
Merge branch 'main' of github.com:microbiome/course_2021_radboud into…
antagomir Jul 8, 2021
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39 changes: 26 additions & 13 deletions 10-material.Rmd
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## 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 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
Expand All @@ -31,15 +37,22 @@ RStudio

## 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)
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

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93 changes: 16 additions & 77 deletions docs/study-material.html
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</head>
Expand Down Expand Up @@ -256,11 +193,15 @@ <h2><span class="header-section-number">10.2</span> Example solutions</h2>
</div>
<div id="r-programming-resources" class="section level2" number="10.3">
<h2><span class="header-section-number">10.3</span> R programming resources</h2>
<p>R progamming</p>
<ul>
<li><a href="https://www.rstudio.com/wp-content/uploads/2016/10/r-cheat-sheet-3.pdf">Base R cheat sheet</a></li>
<li><a href="https://raw.githubusercontent.com/rstudio/cheatsheets/master/base-r.pdf">Base R cheat sheet 2</a></li>
<li><a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheet collection</a></li>
</ul>
<p>Visualization</p>
<ul>
<li>R programming basics: <a href="https://www.rstudio.com/wp-content/uploads/2016/10/r-cheat-sheet-3.pdf">Base R</a></li>
<li>Basics of R programming: <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/master/base-r.pdf">Base R</a></li>
<li><a href="https://www.rstudio.com/resources/cheatsheets/">R cheat sheets</a></li>
<li>R visualization with <a href="https://www.rstudio.com/wp-content/uploads/2016/11/ggplot2-cheatsheet-2.1.pdf">ggplot2</a></li>
<li><a href="https://www.rstudio.com/wp-content/uploads/2016/11/ggplot2-cheatsheet-2.1.pdf">ggplot2 cheat sheet</a></li>
<li><a href="http://www.cookbook-r.com/Graphs/">R graphics cookbook</a></li>
</ul>
<p>Rmarkdown</p>
Expand All @@ -274,22 +215,20 @@ <h2><span class="header-section-number">10.3</span> R programming resources</h2>
</div>
<div id="resources-for-treesummarizedexperiment" class="section level2" number="10.4">
<h2><span class="header-section-number">10.4</span> Resources for TreeSummarizedExperiment</h2>
<ul>
<li>SingleCellExperiment
<ul>
<li><a href="https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">Publication</a></li>
<li><a href="https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html">Project page</a></li>
</ul></li>
<li>SummarizedExperiment
<p>SummarizedExperiment</p>
<ul>
<li><a href="https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html">Publication</a></li>
<li><a href="https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html">Project page</a></li>
</ul></li>
<li>TreeSummarizedExperiment
</ul>
<p>TreeSummarizedExperiment</p>
<ul>
<li><a href="https://f1000research.com/articles/9-1246">Publication</a></li>
<li><a href="https://www.bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.html">Project page</a></li>
</ul></li>
</ul>
<p>SingleCellExperiment</p>
<ul>
<li><a href="https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">Publication</a></li>
<li><a href="https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html">Project page</a></li>
</ul>
</div>
<div id="resources-for-phyloseq" class="section level2" number="10.5">
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