Workshops

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. Participants can take the 4-session workshop at your own pace. Each session includes one recorded video, and a set of data analysis projects on a provided Linux server. You can sign up for office hours at this web site.  

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.   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 session. 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:

Session 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

Session 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

Session 4. Beyond Seurat 

•             Intro to scanpy;

•             Batch effect in data integration;

•             Imputation;

•             Trajectory analysis;

Recorded sessions: video 4