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pkgs.html
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Descriptives
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<h1 class="title toc-ignore">Packages</h1>
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<div id="r" class="section level1 unnumbered">
<h1>R</h1>
<p>Install R, and Rstudio</p>
</div>
<div id="packages" class="section level1 unnumbered">
<h1>Packages</h1>
<p><strong>ggplot2</strong>: For plotting data ggplot2 is very useful - can be installed from CRAN</p>
<p><strong>phyloseq</strong>: There are several packages for handling microbiome type data. For this course we use phyloseq see <a href="https://joey711.github.io/phyloseq/tutorials-index.html">tutorial</a></p>
<p><strong>vegan</strong>: Vegan is a very useful package with a lot of functionality. However, here we use only the adonis() function.</p>
<p><strong>ape</strong>: For handling phylogenetic trees this package is good.</p>
<p><strong>DAtest</strong>: This a custome made <em>single purpose</em> package to be found on <a href="https://github.com/Russel88/DAtest">github</a></p>
<p><strong>DESeq2</strong>: This package is developed for <em>Differential Expression</em> statistics for RNA-seq data. However, it is widely used for microbiome data as well.</p>
<p><strong>metagenomeSeq</strong>: Is a package for handling microbiome data. Here, especially the differential abundance testing procedure featureModel() is used.</p>
<p><strong>ggtree</strong>: A nice vizualisation package for plotting tree, build on top of ggplot2 functionality.</p>
<p>For details on installation and getting-started, please check vignettes, help-documentation, google, youtube,…. Most things are pretty easy to copy-paste and run from examples and then exchange with your own data.</p>
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