tropicalberto/mgc-biosb-singlecellanalysis2020

MGC/BioSB Course - Single Cell Analysis

This week-long course will cover the practicalities of single-cell sample prep and analysis with a particular focus on single-cell RNA-seq libraries. This course is aimed at both wet-lab researchers interested in learning how to analyze their own single-cell data sets, as well as bioinformaticians who are new to single-cell sequencing analysis. Basic knowledge of the programming language R is a prerequisite for participation in the course.

The course features a mix of lectures and practicals, and you will have the opportunity to perform hands-on analysis of scRNA-seq data in R. Topics to be covered in the course include (but not limited to): an overview of different single cell platforms, experimental design, preprocessing of scRNA-seq data, normalization, dimensionality reduction, clustering, batch correction, differential expression, trajectory inference. The fifth day of the course will be a mini-symposium featuring guest lectures from scientists using various single-cell techniques in their research.

Date

19 – 23 October, 2020

On-line course

The course will take place online. For this, we are going to use MS Teams. In the coming days, you will receive an invitation to join the course team. Please note the following:

• Please make sure to download the desktop application (if possible). This usually works better than the web application.
• After clicking on the invitation link, you might need to restart the application to see the course Team in your list of teams.
• In the course team, there are multiple channels. The "Lecture Room" is the main channel where we will have out lecture meetings. Please go there and join the meeting at the time of lectures.
• During the lecture, please make sure you are muted. As much as possible, please keep your camera on. If you want to ask questions, please use the "Raise your hand" button.
• For the Lab sessions, please work on the exercises of the session (on GitHub). If you have questions, post them in the "Questions - Lab Exercises" channel and one of the TAs will answer you as soon as possible. If necessary, you can "meet" the TA in their own channel to have a meeting and share screens.
• Please make sure to join at least 10min early on the first day to ensure that everything works for you.

Programme

Prerequisities

Basic knowledge of the programming language R is a prerequisite for participation in the course.

Software and Data

All participants are required to bring their own laptops for this course. Make sure you have Rstudio and R (v3.5) installed before the course.

To be able to run all code chunks of the course you need to clone or download the course GitHub repository and start an R session in the repository folder. You will also need to install the packages listed here.

Lecturers

• Susan Kloet (LUMC)
• Miao Chien (Erasmus MC)
• Roberta Menafra (LUMC)
• Ahmed Mahfouz (LUMC/TU Delft)
• Marcel Reinders (LUMC/TU Delft)
• Tamim Abdelaal (LUMC/TU Delft)
• Thomas Höllt (LUMC/TU Delft)
• Mohammed Charrout (TU Delft/ LUMC)

Teaching Assistants

• Lieke Michielsen (LUMC/TU Delft)
• Mohammed Charrout (TU Delft/ LUMC)
• Hina Naz Khan (Erasmus MC)
• Mathijs Sanders (Erasmus MC)
• Remco Hoogenboezem (Erasmus MC)

Contact

Ahmed Mahfouz [email protected]