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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>GitHub Package Tutorial</title>
<link rel="stylesheet" href="assets/css/styles.css">
</head>
<body>
<header>
<div class="header-content">
<div class="icon-container">
<img src="assets/images/home_icon1.png" alt="Home Icon 1" class="home-icon">
<img src="assets/images/home_icon2.png" alt="Home Icon 2" class="home-icon">
<img src="assets/images/home_icon3.png" alt="Home Icon 3" class="home-icon">
<img src="assets/images/home_icon4.png" alt="Home Icon 4" class="home-icon">
<img src="assets/images/home_icon5.png" alt="Home Icon 5" class="home-icon">
</div>
<nav>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="about.html">About</a></li>
<li><a href="tutorial.html">Tutorial</a></li>
<li><a href="contact.html">Contact</a></li>
</ul>
</nav>
<img src="assets/images/mouse_icon1.gif" alt="Mouse Icon" class="home-icon"> <!-- New GIF image -->
</div>
</header>
<div class="container">
<div class="sidebar">
<ul class="menu">
<li><a href="#">Data Registration</a>
<ul class="submenu">
<li><a href="#">Image Preprocess</a></li>
<li><a href="#">Reference Slice Reconstruction</a></li>
<li><a href="#">Image Registration with STSHARCQ</a></li>
<li><a href="#">Visualize and Check Registration</a></li>
</ul>
</li>
<li><a href="#">Data Preprocess</a>
<ul class="submenu">
<li><a href="#">Incorporating Anatomical Annotation</a></li>
<li><a href="#">Registration of Experimental Design</a></li>
<li><a href="#">Anatomical Tree Construction</a></li>
</ul>
</li>
<li><a href="#">Cell Typing</a>
<ul class="submenu">
<li><a href="#">Find Baseline Cell Clusters</a></li>
<li><a href="#">Train Classification Model</a></li>
<li><a href="#">Generalized Cell Cluster Identification</a></li>
<li><a href="#">Identify Neurotransmitter Type</a></li>
<li><a href="#">Find Cell Type Marker Gene</a></li>
<li><a href="#">Cell Type Annotation</a></li>
<li><a href="#">Glial Type Annotation</a></li>
<li><a href="#">Manual Check and Refine Annotation</a></li>
<li><a href="#">Classify by Mesostructured Cell Types</a></li>
<li><a href="#">General Type Classification</a></li>
<li><a href="#">Cell Type Visualization</a></li>
</ul>
</li>
<li><a href="#">Atlas Visualization</a>
<ul class="submenu">
<li><a href="#">Adjust Cell Mapping Based on Reference Atlas</a></li>
<li><a href="#">Cell Type Visualization on Atlas</a></li>
<li><a href="#">Neurotransmitter Type Visualization</a></li>
</ul>
</li>
<li><a href="#">Spatial Cell Dynamics</a>
<ul class="submenu">
<li><a href="#">Spatial Cell Type Distribution Comparison and Visualization</a></li>
</ul>
</li>
<li><a href="#">Functional Dynamics</a>
<ul class="submenu">
<li><a href="#">Batch Go Enrichment Screening</a></li>
<li><a href="#">Spatial Go Enrichment</a></li>
</ul>
</li>
<li><a href="#">Communication Dynamics</a>
<ul class="submenu">
<li><a href="#">Cell-Cell Interaction with CellChat2</a></li>
</ul>
</li>
<li><a href="#">Connectivity Dynamics</a>
<ul class="submenu">
<li><a href="#">Inter-regional DEG</a></li>
<li><a href="#">Gene Coexpression Analysis</a></li>
</ul>
</li>
<li><a href="#">Cell Dynamics During Opioid Dependence Formation</a>
<ul class="submenu">
<li><a href="#">Trajectory Matrix Formation</a></li>
<li><a href="#">Control Energy Simulation</a></li>
<li><a href="#">Network Control Energy Visualization</a></li>
</ul>
</li>
<li><a href="#">Cell Dynamics with Neuropsychiatric Gene Set</a>
<ul class="submenu">
<li><a href="#">Extract Gene Set from AnocoDatabase</a></li>
<li><a href="#">Perform Regional to Structural Differential Expression Analysis</a></li>
<li><a href="#">Data Visualization</a></li>
</ul>
</li>
<li><a href="#">Psychiatric Susceptibility Inference by Cell Type Distribution</a>
<ul class="submenu">
<li><a href="#">Cell Type Library Construction</a></li>
<li><a href="#">Model Train</a></li>
<li><a href="#">Back Inference and Visualization</a></li>
</ul>
</li>
</ul>
</div>
<div class="content">
<h1>Official Guidelines to Install and Use CellDynamicST Package to Process Your Spatial Transcriptomic Data</h1>
<p>This website provides a comprehensive tutorial for using our GitHub package.</p>
<!-- Add your data and example figures below -->
<div class="example">
<h2>Example Data and Figures</h2>
<p>Here you can put some of your data and example figures to illustrate the use of your package.</p>
<img src="assets/images/example.png" alt="Example Figure">
</div>
</div>
</div>
<footer>
<p>© 2024 Yihan Xie, all rights reserved.</p>
</footer>
</body>
</html>