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docs/bioinformatics/spatialtranscriptomics.md

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+# Bioinformatics workshops - Fall 2024
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 1</strong></h2>
+
+<p><strong>Sep. 30, Monday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>10X Spatial Transcriptomics (Visium)- </strong>Sample requirements, evaluate sample quality, tissue optimization, sample and library preparation, and library QC and sequencing. Presented by <strong>Amanda Poholek</strong></p>
+
+<p><strong>Demo on 10X genomics cloud analysis</strong>: From FASTQs to biological information with Space Ranger</p>
+
+<p><strong>Running Space Ranger using the CRC cluster:</strong> For fresh frozen samples and formalin fixed paraffin embedded samples Presented by <strong>Dhivyaa Rajasundaram</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 2</strong></h2>
+
+<p><strong>Oct. 1, Tuesday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>Introduction to 10X Visium and Visium HD Data Analysis - </strong>Step by step analysis to correct batch effects between datasets, pre-processing spatial transcriptomics data, identification of spatial features, and spatially variable genes identification.</p>
+
+<p>Basic R knowledge required. Presented by <strong>Silvia Liu</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 3 </strong></h2>
+
+<p><strong>Oct. 2, Wednesday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>Exploring Visium data: Deconvolution and Mapping Methods: </strong>Integrating scRNA-seq and spatial data<strong>. </strong>Cell-type deconvolution of the spatially resolved transcriptome and visualization.</p>
+
+<p>Basic R knowledge required. Presented by <strong>Jiefei Wang</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 4 </strong></h2>
+
+<p><strong>Oct. 3, Thursday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>Cell-Cell Communication Analysis: </strong>Uncover cell-cell communications for spot-based spatially resolved transcriptomics data. Spatially informed ligand-receptor and ligand-receptor-target analysis.</p>
+
+<p>Basic R knowledge required.&nbsp; Presented by <strong>Dhivyaa Rajasundaram</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 5 </strong></h2>
+
+<p><s><strong>Oct. 4, Friday, 1:00pm - 4:00pm</strong></s></p>
+
+<p><span><strong>Oct. 29, Tuesday, 1:00pm-4:00pm (rescheduled)</strong></span></p>
+
+<p><strong>Gene Co-expression Network Estimation for Spatial Transcriptomics: </strong>Cover basics of WGCNA and &nbsp;perform co-expression network analysis on spot-based spatial transcriptomics data.</p>
+
+<p>Basic R knowledge required. Presented by <strong>Jishnu Das</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 6 </strong></h2>
+
+<p><strong>Oct. 7, Monday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>The Single-Cell Spatial Transcriptomics Analysis (ScSTA) Cookbook</strong><br />
+<br />
+This workshop aims to provide attendees with comprehensive knowledge and hands-on experience in the data analysis of sub-cellular resolution single-cell spatial transcriptomics (ScST) technologies such as Nanostring CosMx and 10X Genomics Xenium. We will start with an introduction to the components of ScST, including image registration, cell segmentation, cell type identification, spatial gene expression analysis, and more. A hands-on guided tutorial using real-world lung adenocarcinoma and COVID-19 datasets will follow. Presented by<strong> Arun Das</strong></p>
+
+<h2><strong>Spatial Transcriptomics WORKSHOP 7 </strong></h2>
+
+<p><strong>Oct. 8, Tuesday, 1:00pm - 4:00pm</strong></p>
+
+<p><strong>10X Genomics Xenium data analysis</strong></p>
+
+<p>The hands-on session will provide a solid foundation for handling and analyzing 10x Genomics Xenium datasets. We will begin with the Xenium onboard analysis ranger to conduct initial data exploration and quality assessment. Following this, we will move on to a downstream analysis pipeline using the Seurat workflow, which includes data import, quality control, dimension reduction and clustering, visualization and integration. We will also briefly cover advanced topics including cell segmentation, cell type deconvolution and integration with single cell data. Presented by <strong>Dhivyaa Rajasundaram</strong></p>