PlantSingleCell
🌱 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.
🚀 Quick Start Instructions
Click on each folder to view the step-by-step setup instructions and example files.
📅 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
🧬 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
📅 Day 2: Advanced Methods and Tools
🧠 Section 1: COPILOT – Cell Type Classification with Deep Learning
Presenter: Dr. Wei-Che Hsu
🔬 Section 2: Co-expression Proxy Method
Presenter: Mr. Michael Passalacqua (Cold Spring Harbor Lab)
Explore Coexpression_Proxies on GitHub
🌿 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()
🔁 Section 5: SATURN Method Walk-through
Presenter: Tran Chau
🧾 A step-by-step overview of the SATURN method for cell annotation.
🔗 Click here for detailed setup instructions
We hope this workshop helps you discover the exciting frontier of plant single-cell genomics! 🌾
👥 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! 🎉