🌱 Plant Single Cell Analysis Workshop & Mini-Hackathon

📍 Virginia Tech | Summer Training Camp 🧡🦃

Welcome to the official repository for the Plant Single Cell Analysis summer camp! This 4-day workshop is designed to equip participants with cutting-edge tools, workflows, and insights into plant single-cell transcriptomics.

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🚀 Quick Start Instructions

• 📦 Create Conda Environment
• 📦 Launch Apptainer Demo
• 📦 Launch RStudio Guide

Click on each folder to view the step-by-step setup instructions and example files.

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📅 Day 1: Foundations of Single-Cell Analysis

🧬 Section 1: Read Mapping & Seurat Integration

Presenter: Razan Alajoleen

🧾 Topics Covered:

• Read mapping using ARC
• Loading single-cell data into Seurat

🔗 Click here for detailed setup instructions

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🧬 Section 2: Cross-Sample Integration with Seurat

Presenter: Maryam Haghani

🧾 Topics Covered:

• Sample integration
• UMAP visualization: before vs. after integration
• Gene co-expression of marker genes in Arabidopsis root

🔗 Click here for detailed setup instructions

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📅 Day 2: Advanced Methods and Tools

🧠 Section 1: COPILOT – Cell Type Classification with Deep Learning

Presenter: Dr. Wei-Che Hsu

Explore COPILOT on GitHub

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🔬 Section 2: Co-expression Proxy Method

Presenter: Mr. Michael Passalacqua (Cold Spring Harbor Lab)

Explore Coexpression_Proxies on GitHub

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🌿 Section 3: Orthologous Marker Gene Groups (OMG)

Presenter: Tran Chau

🧾 Topics Covered:

• Cross-species marker gene identification
• Cell type annotation using orthologous gene sets

🔧 To use required packages:

Sys.setenv(R_LIBS_USER="/projects/songli_lab/PlantSingleCell2025/Day_2/env/")
.libPaths(Sys.getenv("R_LIBS_USER"))
.libPaths()

Explore OMG on GitHub

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🔁 Section 5: SATURN Method Walk-through

Presenter: Tran Chau

🧾 A step-by-step overview of the SATURN method for cell annotation.

Explore SATURN on GitHub

🔗 Click here for detailed setup instructions

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We hope this workshop helps you discover the exciting frontier of plant single-cell genomics! 🌾

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👥 Organizers

🔬 Principal Investigator

• Song Li – Associate Professor, Virginia Tech
  Lead organizer and PI for the Plant Single Cell Analysis Workshop

🧑‍💻 Core Organizing Team

• Razan Alajoleen - Postdoctoral Research Associate
• Tran N. Chau - Ph.D. Student
• Maryam Haghani - Ph.D. Student
• Sajib Acharjee Dip - Ph.D. Student
• Sanchari Kundu - Ph.D. Student

Special thanks to all contributors for making the Summer Training Camp a success! 🎉

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