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analysis.html
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The Marshall lab
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<h1 id="software-and-analysis">Software and analysis</h1>
<p>Our research combines wet-lab research with bioinformatic analysis. All code is open-source and is freely available from <a href="http://github.com">github</a>.</p>
<h2 id="featured-software">Featured software</h2>
<h3 id="damidseq_pipeline"><a href="http://owenjm.github.io/damidseq_pipeline">damidseq_pipeline</a></h3>
<p>The damidseq_pipeline software provides automatic alignment, read-extension, normalisation and background reduction for DamID-seq datasets.</p>
<h3 id="poliigenecall"><a href="http://github.com/owenjm/polii.gene.call">polii.gene.call</a></h3>
<p>The polii.gene.call script will call genes with significantly enriched RNA pol II occupancy. It is designed for use with Targeted DamID RNA pol II datasets.</p>
<h3 id="find_peaks"><a href="http://github.com/owenjm/find_peaks">find_peaks</a></h3>
<p>find_peaks is a simple yet robust FDR peak caller. It was designed for use with DamID-seq datasets, but can be used on any file in bedgraph format (including ChIP-seq data).</p>
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