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<h1 id="welcome-to-the-admire-documentation">Welcome to the ADMIRE documentation</h1>
<p>ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.</p>
<p>Use ADMIRE online: <a href="https://bioinformatics.mpi-bn.mpg.de">bioinformatics.mpi-bn.mpg.de</a></p>
<h2 id="overview-and-objective">Overview and Objective</h2>
<p>DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and the stage of a disease. Besides whole genome bisulfit sequencing, Illumina HumanMethylation450K Assays represent a versatile and cost-effective tool to investigate changes of methylation patterns at CpG sites. ADMIRE was developed as an open source, semi-automatic analysis pipeline and visualization tool for Illumina HumanMethylation450K Assays.</p>
<h2 id="features">Features</h2>
<ul>
<li>Automatic filtering and normalization</li>
<li>Statistical testing and multiple testing correction</li>
<li>Supports arbitrary number of samples and sample groups</li>
<li>Differential methylation analysis on pre-calculated and individual genomic regions</li>
<li>Provides ready-to-plug-in files for genome browsers (like IGV)</li>
<li>Provides publication-ready figures for the most differentially methylated regions</li>
<li>Performs gene set enrichment analysis on predefined and individual gene sets</li>
</ul>
<h2 id="how-to-cite">How to cite?</h2>
<p>Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. <em>???</em> (<strong>2015</strong>) when using admire in your work.</p>
<h2 id="contribute">Contribute</h2>
<ul>
<li>Issue Tracker: https://github.molgen.mpg.de/loosolab/admire/issues</li>
<li>Source Code: https://github.molgen.mpg.de/loosolab/admire</li>
</ul>
<h2 id="support">Support</h2>
<p>If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).</p>
<h2 id="license">License</h2>
<p>The project is licensed under the MIT license.</p>
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	<h1 id="welcome-to-the-admire-documentation">Welcome to the ADMIRE documentation</h1>
	<p>ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.</p>
	<p>Use ADMIRE online: <a href="https://bioinformatics.mpi-bn.mpg.de">bioinformatics.mpi-bn.mpg.de</a></p>
	<h2 id="overview-and-objective">Overview and Objective</h2>
	<p>DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and the stage of a disease. Besides whole genome bisulfit sequencing, Illumina HumanMethylation450K Assays represent a versatile and cost-effective tool to investigate changes of methylation patterns at CpG sites. ADMIRE was developed as an open source, semi-automatic analysis pipeline and visualization tool for Illumina HumanMethylation450K Assays.</p>
	<h2 id="features">Features</h2>
	<ul>
	<li>Automatic filtering and normalization</li>
	<li>Statistical testing and multiple testing correction</li>
	<li>Supports arbitrary number of samples and sample groups</li>
	<li>Differential methylation analysis on pre-calculated and individual genomic regions</li>
	<li>Provides ready-to-plug-in files for genome browsers (like IGV)</li>
	<li>Provides publication-ready figures for the most differentially methylated regions</li>
	<li>Performs gene set enrichment analysis on predefined and individual gene sets</li>
	</ul>
	<h2 id="how-to-cite">How to cite?</h2>
	<p>Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. <em>???</em> (<strong>2015</strong>) when using admire in your work.</p>
	<h2 id="contribute">Contribute</h2>
	<ul>
	<li>Issue Tracker: https://github.molgen.mpg.de/loosolab/admire/issues</li>
	<li>Source Code: https://github.molgen.mpg.de/loosolab/admire</li>
	</ul>
	<h2 id="support">Support</h2>
	<p>If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).</p>
	<h2 id="license">License</h2>
	<p>The project is licensed under the MIT license.</p>
	</body>
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