Introduction to scRNA-seq and Data Preprocessing

Dana-Farber Cancer Institute Department of Data Sciences Training Workshop, 02/28/2024

Jeremy M. Simon, Ph.D
Senior Research Scientist, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health

Background

There are many useful applications of single-cell or single-nucleus RNA-seq technologies to better understand cancer biology. In this introductory workshop, we will discuss some of the advantages of adopting single-cell approaches, frequently utilized technologies/platforms, best practices for experimental design, and provide an overview of algorithms used for data preprocessing. We will then provide an interactive demonstration of single-cell/single-nucleus RNA-seq data preprocessing with alevin-fry, resulting in a counts matrix ready for downstream analysis

Example data used for workshop

10X Genomics, 1k PBMC, 3' V3 chemistry

Contents

Powerpoint slides, quarto markdown containing all (bash, R) code, as well as output from AlevinQC
HTML containing markdown and figures deployed here

External links

This session was recorded live and the full session (2 hrs) is available on YouTube here