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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, shrink-to-fit=no">
<meta name="generator" content="Hugo 0.114.1">
<title>StereoSeq Data Workflow</title>
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<a class="navbar-brand" href="#">StereoSeq Data Workflow</a>
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<div class="container mt-4">
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<h3>Navigation</h3>
<ul class="nav flex-column">
<li class="nav-item"><a href="#preparation" class="nav-link">Preparation</a></li>
<li class="nav-item"><a href="#loadData" class="nav-link">Load Data</a></li>
<li class="nav-item"><a href="#Quality Control" class="nav-link">Quality Control</a></li>
<li class="nav-item"><a href="#Normalization" class="nav-link">Normalization</a></li>
<li class="nav-item"><a href="#Preprocessing" class="nav-link">Preprocessing</a></li>
<li class="nav-item"><a href="#Clustering" class="nav-link">Clustering</a></li>
<li class="nav-item"><a href="#Expression Enhancement" class="nav-link">Expression Enhancement</a></li>
<li class="nav-item"><a href="#Spatially variable genes identification" class="nav-link">Spatially variable genes identification</a></li>
<li class="nav-item"><a href="#Spatial Domain Detection" class="nav-link">Spatial Domain Detection</a></li>
<li class="nav-item"><a href="#Cell Type Annotation" class="nav-link">Cell Type Annotation</a></li>
<li class="nav-item"><a href="#Cell Segmentation" class="nav-link">Cell Segmentation</a></li>
<li class="nav-item"><a href="#Cell–cell communications" class="nav-link">Cell–cell communications</a></li>
</ul>
</div>
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<!-- Main Content -->
<div class="col-md-10 content-section">
<h1 class="mb-4">StereoSeq Data Workflow</h1>
<h2 class="mb-4" style="font-size: 20px">Created by Stomics US Data Team</h2>
<p>This is a StereoSeq data analysis workflow. This demonstration will use a data set <a href="http://116.6.21.110:8090/share/21bb9df9-e6c5-47c5-9aa8-29f2d23a6df4" target="_blank" rel="noopener noreferrer">SS200000135TL_D1</a> of a mouse brain.</p>
<div style="text-align: center;">
<img src="images/Image_20240927214042.png" alt="Description of image" style="width:300px; height:auto;">
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<div class="container mt-5" id="preparation">
<h2 id="preparation" class="mt-5">Preparation</h2>
<p>In this section, we will go over the preparation steps necessary to run the StereoSeq data analysis. This includes setting up the environment and installing the required tools and dependencies.</p>
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<img src="images/preparation_image.png" alt="Preparation Image" style="width:400px; height:auto;">
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<h3>Environment Setup</h3>
<p>Ensure that the following dependencies are installed:</p>
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<pre><code class="language-bash">
# Install necessary packages
conda create -n stereoSeq_env python=3.8
conda activate stereoSeq_env
pip install numpy pandas scanpy
</code></pre>
</div>
<h3>Data Download</h3>
<p>Download the required dataset:</p>
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<pre><code class="language-bash">
# Download the dataset
wget http://example.com/dataset/SS200000135TL_D1.zip
unzip SS200000135TL_D1.zip
</code></pre>
</div>
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