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<!DOCTYPE html>
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<li><a href="methylomes.html">Methylome Resource</a></li>
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<h1 class="mt-4 mb-3">Tutorials <!-- <small>Subheading</small> --></h1>
<div class="row">
<div class="col-md-12">
<h2>RnBeadsDJ -- A Graphical User Interface for RnBeads</h2>
<p>
This tutorial introduces RnBeadsDJ, a graphical user interface to configure and run RnBeads analyses
</p>
<p>
A vignette providing step-by-step instructions on how to run the tutorial is available <a href="./materials/data/tutorial/RnBeadsDJ/RnBeads_GUI_quickstart.pdf">here</a>.
</p>
<h3>1. Download the Datasets</h3>
<p> Download and extract the following file:</p>
<ul>
<li><a href="./materials/data/tutorial/epigenomics2016/Ziller2011_PLoSGen_450K.zip">Download the Ziller 450K dataset (381 MB)</a></li>
</ul>
<p>
<h3>2. Install R</h3>
<p>Visit the <a href="http://cran.cnr.berkeley.edu/">CRAN website</a> and download the version of R corresponding to your platform. Install R using the downloaded executable.</p>
<h3>3. Install RnBeads and Ghostscript</h3>
<p>You can find detailed instructions on how to install RnBeads and ghostscript following this <a href="data/installing_rnbeads.html">link</a>.</p>
<h3>4. Analyze Your Methylome Data Using RnBeads</h3>
<p>Follow the instructions provided in the <a href="./materials/data/tutorial/RnBeadsDJ/RnBeads_GUI_quickstart.pdf">tutorial vignette</a>.</p>
<h3>Example Reports</h3>
<p>Reports for the examples discussed in the tutorial are available here:</p>
<ul>
<li><a href="./materials/reports/tutorial/RnBeadsDJ/results/report_Ziller2011/index.html">Ziller2011 450K data analysis</a></li>
</ul>
</div>
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<hr>
<div class="row">
<div class="col-md-12">
<h2>Epigenomics 2016</h2>
<p>
This tutorial contains instructions and material for the workshop on <i>"Analyzing Methylome Data using RnBeads"</i> that was presented at the Epigenomics 2016 (Puerto Rico) meeting.
To get R and RnBeads set up for the tutorial and to retrieve the example data, please follow steps 1, 2 and 3 described below. Afterwards, feel free to experiment with the code contained in the downloaded data directory.
</p>
<p>
The presentation slides from the workshop are available <a href="./materials/data/tutorial/epigenomics2016/epigenomics2016_workshop_rnbeads_20160201.pdf">here</a>.
</p>
<h3>1. Download the Tutorial Scripts and Datasets</h3>
<p> Download and extract the following file for the tutorial:</p>
<ul>
<li><a href="./materials/data/tutorial/epigenomics2016/epigenomics2016.zip">Download the tutorial data pack (720 MB)</a></li>
</ul>
<p>
If you don't want to download the entire data package at once, you can also download the files individually:
</p>
<ul>
<li><a href="./materials/data/tutorial/epigenomics2016/epigenomics2016_code.zip">Download the tutorial source code (15 KB)</a></li>
<li><a href="./materials/data/tutorial/epigenomics2016/Ziller2011_PLoSGen_450K.zip">Download the Ziller 450K dataset (381 MB)</a></li>
<li><a href="./materials/data/tutorial/epigenomics2016/Bock2012_MolCell_RRBS.zip">Download the Bock RRBS dataset (336 MB)</a></li>
</ul>
<h3>2. Install R</h3>
<p>Visit the <a href="http://cran.cnr.berkeley.edu/">CRAN website</a> and download the version of R corresponding to your platform. Install R using the downloaded executable.</p>
<h3>3. Install RnBeads and Ghostscript</h3>
<p>You can find detailed instructions on how to install RnBeads and ghostscript following this <a href="data/installing_rnbeads.html">link</a>.</p>
<h3>4. Analyze Your Methylome Data Using RnBeads</h3>
<p>Follow the instructions provided in the presentation.</p>
<h3>Example Reports</h3>
<p>Reports for the examples discussed in the tutorial are available here:</p>
<ul>
<li><a href="./materials/reports/tutorial/epigenomics2016/results/report_Ziller2011_vanilla/index.html">Ziller2011 450K data analysis</a></li>
<li><a href="./materials/reports/tutorial/epigenomics2016/results/report_Bock2012_vanilla/index.html">Bock2012 RRBS data analysis</a></li>
</ul>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-12">
<a name="agePredTutorial"></a>
<h2>Age Prediction Using RnBeads</h2>
<p>
Here, we provide instructions for how to use the epigenetic age prediction tool MethylAger. MethylAger was created as an RnBeads module and is therefore applicable to all DNA methylation assays operating at single base pair resolution. MethylAger contains several predefined predictors that were extensively evaluated for the most frequently used DNA methylation assays (e.g. 27K, 450K and RRBS). Depending on the type of the input data set, MethylAger decides which of these predictors is applicable. Additionally, a custom predictor can be created from the provided data set. For a detailed description of the methods employed and of the predefined predictors explore <a href="ageprediction.html">this website</a>. Similar to the tutorial described above, an installation of R is needed. Then follow the instructions and enjoy the functions of the epigenetic age prediction tool MethylAger.
</p>
<h3>1. Download R Tutorial and Data Set</h3>
<p>
The data package, including the R tutorial and an example data set can be downloaded <a href="./materials/data/methylager/methylager_tutorial.zip">here (233 MB)</a>.
</p>
<h3>2. Use MethylAger</h3>
<p>
Follow the instructions provided in the R tutorial and analyze the example data set to get used to MethylAger.
</p>
<h3>Additional Information</h3>
<ul>
<li><a href="./materials/data/methylager/methylager_tutorial.html">HTML report created by the tutorial</a></li>
<li><a href="./materials/data/methylager/analysis_set.zip">Data set used in the analysis (233 MB)</a></li>
<li><a href="./materials/data/methylager/complete_report/covariate_inference.html">Example covariate inference report</a></li>
</ul>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-12">
<h2>Joint analysis of Illumina EPIC v1 and EPIC v2 array data</h2>
<p>
This brief vignette demonstrates a cross-platform integration of DNA methylation data from Illumina EPIC v1 and EPIC v2 microarrays.
<ul>
<li><a href="./materials/data/tutorial/tutorial_EPICv1_v2/tutorial.html">View the tutorial</a></li>
</ul>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-12">
<h2>Cross-platform analysis with RnBeads</h2>
<p>
This tutorial is a brief demo of the new functionality for the joint storage and analysis of data from different DNA methylation profiling platforms. The updated <code>combine</code> method enables pair-wise merging of all classes of data containers. Obtained hybrid data sets can be used for any standard RnBeads analysis. The tutorial demonstrates new functionality using pubicly available data of primary prostate cancer samples and cell lines from the EPIC array evaluation study <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1066-1">[Pidsley et al., Genome Biology, 2016]</a>
<ul>
<li><a href="./materials/data/tutorial/cross_platform/tutorial.html">View the tutorial</a></li>
</ul>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-12">
<h2>Support for Additional Genome Assemblies</h2>
<p>RnBeads relies on annotation packages – one for every supported genome assembly. The ones currently supported are <b>hg19</b>, <b>hg38</b>, <b>mm9</b>, <b>mm10</b> and <b>rn5</b>. If you would like to analyze a different genome, you need to create a new annotation package. <a href="https://github.com/epigen/RnBeadsAnnotationCreator">RnBeadsAnnotationCreator</a> facilitates the generation of annotation packages for RnBeads.</p>
<p>A dedicated vignette (<a href="data/RnBeadsAnnotationCreator.pdf">download PDF</a>) explains how RnBeads annotation packages are structured and includes a tutorial on creating an annotation package for the Zebrafish genome.</p>
</div>
</div>
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<div class="col-md-12">
<h2>Integration with DiMmeR</h2>
<p>RnBeads, by default, uses <a href="https://academic.oup.com/nar/article/43/7/e47/2414268">limma</a> for performing differential methylation analysis. Alternatively, RnBeads now integrates with <a href="https://academic.oup.com/bioinformatics/article/33/4/549/2593589">DiMmeR</a> for performing such an analysis. The tutorial below guides you through the analysis.</p>
<ul>
<li><a href="data/Dimmer.html">View the tutorial</a></li>
</ul>
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