6-10 June 2022
This course will be held online in response to the coronavirus outbreak.
This course will introduce biologists and bioinformaticians to the field of single-cell RNA sequencing. We will cover a range of software and analysis workflows that extend over the spectrum from
the best practices in the filtering scRNAseq data
to the downstream analysis of cell clusters and temporal ordering. This course will help the attendees gain accurate insights in pre-processing, analysis and interpretation of scRNAseq data.
We will start by introducing general concepts about single-cell RNA-sequencing. From there, we will then continue to describe the main analysis steps to go from raw sequencing data to processed and usable data. Finally, we will focus more specifically on the different analyses strategies to use in order to extract information from genomic datasets such as Hi-C, ATAC-seq or ChIP-seq.
Throughout the workshop, bash tools and R/Bioconductor packages will be used to analyse datasets and learn new approaches.
The course is structured in modules over five days. Each day will include formal lectures covering the key concepts required to understand scRNAseq analysis. The remainder of each day will consist in practical hands-on sessions focusing on analysis of scRNA-seq data. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill, as well as applying these skills on your own to complete individual exercises.
During and after each exercise, interpretation of results will be discussed as a group.
The course will be mostly beneficial to those who have, or will shortly have, scRNA-seq data ready to analyse.
The material is suitable both for experimentalists who want to learn more about data-analysis as well as computational biologists who want to learn about scRNASeq methods.
Examples demonstrated in this course can be applied to any experimental protocol or biological system.
The requirements for this course are:
At the end of this course, you should be able to:
Throughout the course, we will also have a focus on reproducible research, documented content and interactive reports.
Monday– Classes from 2-8 pm CE
Lecture 1 – scRNA-Seq experimental design
Lecture 2 - Intro to Data processing: from bcl file to count matrix
Lab 1 – Familiarizing yourself with the course AWS instance
Lab 2 – Processing raw scRNA-Seq data
Dr. Orr Ashenberg (Broad Institute, USA)
Dr. Jacques Serizay (Institut Pasteur, FR)
> 30 days before the start date = 30% cancellation fee
< 30 days before the start date= No Refund.
Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.