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. This mini-symposium will be organized together with the Single Cell Network Leiden (scNL).

18 – 22 October, 2021

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.
• Do not start a new meeting yourself.
• 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.
• After the lecture ends, please make sure you leave the meeting. Otherwise, the meeting remains open (organizers cannot force close it).
• 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.

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

For this course, we make use of RStudio Cloud. All you need for this is a browser. You will receive more instructions at the beginning of the course.

• Susan Kloet (LUMC)
• Miao Chien (Erasmus MC)
• Roberta Menafra (LUMC)
• Ahmed Mahfouz (LUMC/TU Delft)
• Tamim Abdelaal (LUMC/TU Delft)
• Thomas Höllt (LUMC/TU Delft)
• Mohammed Charrout (TU Delft/ LUMC)
• Lieke Michielsen (LUMC / TU Delft)
• Anna Alemany (LUMC)

• Lieke Michielsen (LUMC/TU Delft)
• Mohammed Charrout (TU Delft/ LUMC)
• Hina Naz Khan (Erasmus MC)
• Gregory van Beek (Erasmus MC)
• Remco Hoogenboezem (Erasmus MC)
• Chiel Wevers (Erasmus MC)

Ahmed Mahfouz A.Mahfouz@lumc.nl