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<html><!-- InstanceBegin template="/Templates/design_template.dwt" codeOutsideHTMLIsLocked="false" -->
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<title>Resources</title>
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<a class="navbar-brand text-center" style="font-size: 14px;"><h2 style="text-shadow: 2px 2px 2px #AABEC6;"><u>MontgomeryLab</u></h2><p class="shadow-text">Stanford University at School of Medicine</p></a>
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<p><a class="btn text-primary pl-0" target="_blank" href="https://github.com/boxiangliu/ANTseq/"><strong>ANT-seq</strong></a> <span class="small">Ancestry inference through microfluidic multiplex PCR and targeted sequencing</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="https://github.com/davidaknowles/eagle"><strong>EAGLE</strong></a> <span class="small">Detection of GxE interactions in transcriptome data</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="https://github.com/joed3/eigenMT"><strong>EigenMT</strong></a> <span class="small">An efficient multiple hypothesis testing correction for eQTLs</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://techhouse.org/~tracy/ipf.html"><strong>IPF Gene Explorer</strong></a> <span class="small">A web server for investigating differential expression and splicing in idiopathic pulmonary fibrosis lung tissue.</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="resources/mmPCRScript_forRelease.11.2014.tar.gz"><strong>mmPCR-Seq Primer Design scripts</strong></a> <span class="small"></span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://www.oreganno.org"><strong>ORegAnno: Open Regulatory Annotation Database</strong></a> <span class="small">A database of literature curated gene regulatory elements and regulatory variants.</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="resources/pathscan.zip"><strong>Path-scan</strong></a> <span class="small">A reporting tool for identifying clinically actionable variants.</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://52.37.206.146:7998/"><strong>Sardinia eQTL browser</strong></a> <span class="small">Browse Sardinian eQTLs from Pala, Zappala et al.</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://52.37.206.146:7999/"><strong>Cross population eQTL Explorer</strong></a> <span class="small">Browse Cross population eQTLs</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://52.37.206.146:8000/"><strong>Sex-specific eQTL browser</strong></a> <span class="small">Browse sex-specific eQTLs from Kukurba et al.</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="http://smweb.bcgsc.ca"><strong>Sockeye, Chinook and CHuM</strong></a> <span class="small">3D genome visualization, peer-to-peer bioinformatics and machine-learning for regulatory variation (pre-2006).</span></p>
<p><a class="btn text-primary pl-0" target="_blank" href="resources/spliceplot/index.html"><strong>SplicePlot</strong></a> <span class="small">A tool for visualizing splicing quantitative trait loci (sQTL).</span></p>
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<p style="padding-top: 10px;">Liu et al, <strong>Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci</strong> - <a target="_blank" href="https://stanford.box.com/s/e6e8hyft5u7wix1nzg5mjfqa084c4tin">eQTL and sQTL summary statistics</a></p>
<p>Pala, Zappala et al, Nature Genetics, 2017 <strong>"Individual- and population-specific regulatory variation in Sardinia"</strong> - <a target="_blank" href="https://github.com/zaczap/sardinia">supplemental code/info page</a></p>
<p>Kukurba et al.,, PloS Genetics, 2013 <strong>"Allelic expression of deleterious protein-coding variants across human tissues"</strong> - <a target="_blank" href="resources/kukurba2013/index.html">supplemental info page</a></p>
<p>Montgomery et al., Nature, 2010 <strong>"Transcriptome genetics using second generation sequencing in a Caucasian sample"</strong> - <a target="_blank" href="http://jungle.unige.ch/rnaseq_CEU60/">supplemental info page</a></p>
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<p style="padding-top: 10px;"> <a target="_blank" href="https://gregor.stanford.edu/">GREGoR website</a></p>
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