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Workshops

Single-cell RNAseq Analysis Workshop  
February 12 2024 - March 4 2024

Hands-on computer assignment. 

This workshop is jointly hosted by the Bioinformatics Facility and Genomics Facility of Cornell Institute of Biotechnology. It will cover basic skills to analyze single-cell RNAseq data. During the 4 week workshop, each participant will attend one Zoom lecture per week (3:00PM every Monday, followed by guided hands-on at 4:00PM), and finish a set of data analysis projects on a provided Linux server. Office hours (Zoom) will be provided during and after the workshops. 

Pre-requisites:

Basic Linux command line and R skills are required to take this workshop. If you are not familiar with Linux operating system, you can take this beginners' workshop, or the more extensive three-session Linux workshop. If you have no experience with R, there are beginners' R workshops (Jan 25th & 29th) by Cornell CSCU.   During this SC RNAseq workshop, we will provide step-by-step instructions how to finish the projects, and some guidance how to do Linux and R. Python package Scanpy will be introduced in the 4th week. Python coding skill is not required during the workshop, but you will need to develop Python skill in order to analyze your own data using Scanpy. 

Syllabus:

Week 1. Single cell technology, from samples to raw data to count matrix

•             Intro to single-cell technologies, including experimental design and expectations;

•             Using 10x cellranger count for gene expression;

•             Using 10x Loupe browser for exploration of results;

Recorded sessions: video 1

Week 2,3. Biological data analysis in Seurat part 1 and part 2 

•             Data structure, filtering and basic QC;

•             Sample normalization, integration and clustering;

•             Markers for cell type identification;

•             Comparative analysis between populations of cells;

•            Gene set analysis;

•             Visualization;

Recorded sessions: video 2 video 3

Week 4. Beyond Seurat 

•             Intro to scanpy;

•             Batch effect in data integration;

•             Imputation;

•             Trajectory analysis;

Recorded sessions: video 4

Workshop Outline  
Session 1 Feb 12 2024 3:00PM - 5:00PM
Single cell technology, from samples to raw data to count matrix. Download: slides, hands-on Video: video 1
Session 2 Feb 19 2024 3:00PM - 5:00PM
Biological data analysis  - part 1 Download: slides, hands-on Video: video 2
Session 3 Feb 26 2024 3:00PM - 5:00PM
Biological data analysis  - part 2 Download: slides, hands-on Video: video 3
Session 4 Mar 4 2024 3:00PM - 5:00PM
Beyond Seurat Download: slides, hands-on Video: video 4  
Session 5 Mar 6 2024 12:00PM - 12:00PM
Extra hands on:   From Seurat to Loupe    Exporting Seurat to SingleCellExperiment object
 
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