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<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
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<a href="/#about" data-target="#about">
<span>Home</span>
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<span>Publications</span>
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<a href="/#posts" data-target="#posts">
<span>Posts</span>
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<span>Teaching</span>
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<span>Contact</span>
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<div class="row" itemprop="author" itemscope itemtype="http://schema.org/Person" itemref="person-email person-address">
<div class="col-xs-12 col-md-4">
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</div>
<meta itemprop="image" content="https://guangchuangyu.github.io/img/portrait.jpg">
<div class="portrait-title">
<h2 itemprop="name">Guangchuang YU</h2>
<h3 itemprop="jobTitle">Postdoc researcher</h3>
<h3 itemprop="worksFor" itemscope itemtype="http://schema.org/Organization">
<a href="http://www.hku.hk/" target="_blank" itemprop="url">
<span itemprop="name">The University of Hong Kong</span>
</a>
</h3>
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<link itemprop="url" href="https://guangchuangyu.github.io/">
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<div class="col-xs-12 col-md-8" itemprop="description">
<h1 id="biography">Biography</h1>
<p>I am a postdoc researcher in School of Public Health at The University of Hong
Kong. I am broadly interested in bioinformatics, metagenomics and molecular
evolution especially phylogenetic dynamics of influenza A virus.</p>
<p>I love the R programming language and have
contributed <a href="https://guangchuangyu.github.io/software/" target="_blank">9 Bioconductor packages</a>
to the community.</p>
<div class="row">
<div class="col-sm-5">
<h3>Interests</h3>
<ul class="ul-interests">
<li>Bioinformatics</li>
<li>Metagenomics</li>
<li>Molecular Evolution</li>
<li>Visualization</li>
</ul>
</div>
<div class="col-sm-7">
<h3>Education</h3>
<ul class="ul-edu fa-ul">
<li>
<i class="fa-li fa fa-graduation-cap"></i>
<div class="description">
<p class="course">PhD in Molecular Evolution, 2017</p>
<p class="institution">The University of Hong Kong</p>
</div>
</li>
<li>
<i class="fa-li fa fa-graduation-cap"></i>
<div class="description">
<p class="course">Master in Biochemistry and Molecular Biology, 2009</p>
<p class="institution">Anhui Medical University</p>
</div>
</li>
<li>
<i class="fa-li fa fa-graduation-cap"></i>
<div class="description">
<p class="course">BSc in Biotechnology, 2005</p>
<p class="institution">South China Agricultural University</p>
</div>
</li>
</ul>
</div>
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</section>
<section id="publications_selected" class="home-section">
<div class="container">
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<div class="col-xs-12 col-md-4 section-heading">
<h1>Selected Publications</h1>
</div>
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<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<a href="https://guangchuangyu.github.io/publication/ggtree/">
<img src="/img/C2mxyBuUcAEt391.jpg" class="pub-banner"
itemprop="image">
</a>
</div>
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
<a href="https://guangchuangyu.github.io/publication/ggtree/" itemprop="url">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>
</h3>
<div class="pub-abstract" itemprop="text">
1.We present an R package, GGTREE, which provides programmable visualization and annotation of phyloge- netic trees. 2. GGTREE can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other R packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of BEAST, EPA, HYPHY, PAML, PHYLODOG, PPLACER, R8S, RAXML and REVBAYES software, and allows using these data to annotate the tree. 3. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulat- ing a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxo- nomic units and exploration of a large tree by zooming into a selected portion. 4. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. 5. The package GGTREE is released under the ARTISTIC-2.0 LICENSE. The source code and documents are freely available through BIOCONDUCTOR (http://www.bioconductor.org/packages/ggtree).
</div>
<div class="pub-authors" itemprop="author">
<strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>
</div>
<div class="pub-publication">
<em>MEE</em>
</div>
<div class="pub-links">
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/publication/ggtree/">
Details
</a>
<a class="btn btn-primary btn-outline btn-xs" href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract">
PDF
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar">
Slides
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/">
Video
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://github.com/GuangchuangYu/ggtree">
Code
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/">
Dataset
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/ggtree/">
Project
</a>
</div>
</div>
</div>
</div>
<div class="pub-list-item" itemscope itemtype="http://schema.org/CreativeWork">
<div class="row">
<div class="col-md-12">
<h3 class="article-title" itemprop="name">
<a href="https://guangchuangyu.github.io/publication/chipseeker/" itemprop="url">ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization</a>
</h3>
<div class="pub-abstract" itemprop="text">
Summary: ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with user's own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation.
</div>
<div class="pub-authors" itemprop="author">
<strong>G Yu</strong>, LG Wang, QY He<sup>*</sup>
</div>
<div class="pub-publication">
<em>Bioinformatics</em>
</div>
<div class="pub-links">
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/publication/chipseeker/">
Details
</a>
<a class="btn btn-primary btn-outline btn-xs" href="http://bioinformatics.oxfordjournals.org/content/31/14/2382">
PDF
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://github.com/GuangchuangYu/ChIPseeker">
Code
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/ChIPseeker/">
Project
</a>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="publications" class="home-section">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-4 section-heading">
<h1>Recent Publications</h1>
<p class="view-all">
<a href="/publication/">
More Publications
<i class="fa fa-angle-double-right"></i>
</a>
</p>
</div>
<div class="col-xs-12 col-md-8">
<ul class="fa-ul">
<li itemscope itemtype="http://schema.org/CreativeWork">
<i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i>
<span itemprop="name">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</span>
<p>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/publication/ggtree/">
Details
</a>
<a class="btn btn-primary btn-outline btn-xs" href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract">
PDF
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar">
Slides
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/">
Video
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://github.com/GuangchuangYu/ggtree">
Code
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/">
Dataset
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/ggtree/">
Project
</a>
</p>
</li>
<li itemscope itemtype="http://schema.org/CreativeWork">
<i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i>
<span itemprop="name">ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization</span>
<p>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/publication/reactomepa/">
Details
</a>
<a class="btn btn-primary btn-outline btn-xs" href="http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e">
PDF
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://github.com/GuangchuangYu/ReactomePA">
Code
</a>
<a class="btn btn-primary btn-outline btn-xs" href="https://guangchuangyu.github.io/ReactomePA/">
Project
</a>
</p>
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