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Software.html
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<!DOCTYPE HTML>
<!--
Iridium by TEMPLATED
templated.co @templatedco
Released for free under the Creative Commons Attribution 3.0 license (templated.co/license)
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<html>
<head>
<title>Danko Lab</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="" />
<meta name="keywords" content="" />
<link href='http://fonts.googleapis.com/css?family=Arimo:400,700' rel='stylesheet' type='text/css'>
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<body>
<!-- Header -->
<div id="header">
<div class="container">
<!-- Logo -->
<div id="logo">
<h1><a href="#">Danko Lab</a></h1>
<!--<span>Website coming soon!</span>-->
</div>
<!-- Nav -->
<nav id="nav">
<ul>
<li><a href="index.html">Homepage</a></li>
<li><a href="Research.html">Research</a></li>
<li><a href="Team.html">Team</a></li>
<li><a href="Publications.html">Publications</a></li>
<li class="active"><a href="Software.html">Software</a></li>
<li><a href="Contact.html">Find Us</a></li>
</ul>
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<div id="content" class="2u skel-cell-important"><BR></div>
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<div id="content" class="8u skel-cell-important">
<section>
<header>
<h2>Software</h2>
<span class="byline">Bioinformatics Software <a href="https://github.com/danko-lab">[GitHub]</a>.</span>
</header>
<BR>
<div class="row">
<div class="5u">
<img src="images/BayesPrism-Logo-Small.png" alt="" />
</div>
<div class="6u">
<p><a title="[BayesPrism]" href="https://dreg.dnasequence.org/"><strong>BayesPrism.</strong></a> Try the (Beta!) BayesPrism web server! <BR>
Paper: <a title="[Nature Cancer]" href="https://www.nature.com/articles/s43018-022-00356-3">Nature Cancer.</a><BR>
Source code here: <a title="[GitHub]" href="https://github.com/Danko-Lab/BayesPrism">BayesPrism [GitHub].</a></p>
</div>
</div>
<div class="row">
<div class="5u">
<img src="images/dREG-gateway-logo-muted-small.png" alt="" />
</div>
<div class="6u">
<p><a title="[dREG]" href="https://dreg.dnasequence.org/"><strong>dREG Science Gateway.</strong></a> dREG now has a web server! Try it out. <BR>
Paper: <a title="[Genome Research]" href="https://genome.cshlp.org/content/29/2/293.short">Genome Research.</a><BR>
Source code here: <a title="[GitHub]" href="https://github.com/Danko-Lab/dREG">dREG [GitHub].</a></p>
</div>
</div>
<div class="row">
<div class="2u">
<img src="images/rtfbsdb.png" alt="" />
</div>
<div class="4u">
<p><a title="[GitHub]" href="https://github.com/Danko-Lab/rtfbs_db"><strong>RTFBSDB [GitHub].</strong></a> Parse TF motifs from public databases, read into R, and scan using 'rtfbs'. <br>
Paper: <a title="[Full text]" href="http://bioinformatics.oxfordjournals.org/content/32/19/3024">Bioinformatics.</a></p>
</div>
<div class="2u">
<img src="images/AlleleHMM-small.png" alt="" />
</div>
<div class="4u">
<p><a title="[GitHub]" href="https://github.com/Danko-Lab/AlleleHMM"><strong>AlleleHMM [GitHub].</strong></a> Find allele-specific signal in distributed functional genomic data. <br> Paper: <a title="[Nucleic Acids Research]" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz176/5421125">Nucleic Acids Research.</a></p>
</div>
</div>
<div class="row">
<div class="2u">
<img src="images/groHMM.png" alt="" />
</div>
<div class="4u">
<p><a title="[Bioconductor]" href="http://www.bioconductor.org/packages/release/bioc/html/groHMM.html"><strong>groHMM [Bioconductor].</strong></a> Segment genomic data using hidden Markov models. Updated and maintained by the <a href="http://www.utsouthwestern.edu/education/medical-school/departments/green-center/members-labs/kraus-lab.html">Kraus lab</a>.</p>
</div>
<div class="2u">
<img src="images/AffyTiling.png" alt="" />
</div>
<div class="4u">
<p><a title="[Bioconductor]" href="http://www.bioconductor.org/packages/2.12/bioc/html/AffyTiling.html"><strong>AffyTiling [Bioconductor].</strong></a> Easy extraction of individual probes in Affymetrix tiling arrays.</p>
</div>
</div>
<div class="row">
<div class="2u">
<img src="images/Rgtsvm.png" alt="" />
</div>
<div class="4u">
<p><a title="[GitHub]" href="https://github.com/Danko-Lab/Rgtsvm"><strong>Rgtsvm [GitHub].</strong></a> R package for fitting and evaluating support vector machines (SVMs) using GPU hardware. e1071 compatible.</p>
</div>
<div class="2u">
<img src="images/dREG.Preprint.png" alt="" />
</div>
<div class="4u">
<p><a title="[GitHub]" href="https://github.com/Danko-Lab/tfTarget"><strong>tfTarget [GitHub].</strong></a> tfTarget is a unified framework that identifies the "TF -> TRE -> target gene" networks.</p>
</div>
</div>
</section>
</div>
<div id="content" class="2u skel-cell-important"><BR></div>
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</div>
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<div class="4u">
<section>
<h2>Danko Lab</h2>
<ul class="contact">
<li>
<span class="mail">E-Mail</span>
<span>
<script type="text/javascript" language="Javascript">// <![CDATA[Hide script from non-javascript-enabled browsers
var username="dankoc";
var at="@";
var domain="gmail.com";
document.write("<a href='mailto:" +username+""+at+""+domain+ "'>" + username+""+at+""+domain + "</a>");
</script>
</span>
</li>
<li>
<span class="mail">Social</span>
<a href="https://genomic.social/@charlesdanko"><img src="images/Mastodon-24-24.png" alt="" /></a>
<a href="https://twitter.com/charlesdanko"><img src="images/twitter.png" alt="" /></a>
<a href="https://github.com/danko-lab"><img src="images/github.png" alt="" /></a>
</li>
<li>
<span class="address">Address</span>
<span>
The Baker Institute for Animal Health<br />
College of Veterinary Medicine <br />
Cornell University <br />
Hungerford Hill Road<br />
Ithaca, NY 14853
</span>
</li>
</ul>
</section>
</div>
<div class="4u">
<section>
<h2>Cornell University</h2>
<ul class="default">
<li><a href="https://www2.vet.cornell.edu/departments-centers-and-institutes/baker-institute">The Baker Institute</a></li>
<li><a href="http://www.vet.cornell.edu/biosci/">Department of Biomedical Sciences</a></li>
<li><a href="http://www.vet.cornell.edu/">College of Veterinary Medicine</a></li>
<li><a href="http://www.cb.cornell.edu/">Computational Biology Graduate Program</a></li>
<li><a href="http://www.cornell.edu">Cornell University</a></li>
</ul>
</section>
</div>
<div class="4u">
<section>
<h2>Join the lab!</h2>
<ul class="contact">
<li>
<span>We are considering applications from exceptionally talented scientists!</span>
</li>
<li>
<span class="mail">Postdocs:</span>
<span>E-mail a 1 page cover letter, a curriculum vitae, and 3 letters of reference to Charles Danko.</span>
</li>
<li>
<span class="mail">Students:</span>
<span>Apply through the graduate fields of <a href="http://www.cb.cornell.edu/">Computational Biology</a> or <a href="http://www.gendev.cornell.edu/">Genetics, Genomics & Development</a>.</span>
</li>
</ul>
</section>
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</div>
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