Single-Cell Transcriptomics with R

The course is now full with a long waiting list. If you do not want to miss your chance to be part of the next session and remain informed about all training activities at SIB, we highly recommend you to keep an eye on our list of upcoming events (https://www.sib.swiss/training/upcoming-training-courses) and subscribe to our courses mailing list here (if not yet done): https://lists.sib.swiss/mailman/listinfo/courses. Thank you for your understanding.

Overview

In contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expression at a whole population level, single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression profile at a single cell resolution while enabling the discovery of tissue specific subpopulations and markers. For example, contrasting different sample conditions i.e. disease vs. normal using scRNAseq can help identify sub-cellular differential behaviours and thus target specific gene markers. This 3-day course will cover the main technologies as well main aspects to consider while designing a scRNAseq experiment including a hands-on practical data analysis session applied to droplet-based methods. The training materials for this course are in its dedicated GitHub page.

Audience

This course is intended for life scientists and bioinformaticians familiar with "Next Generation Sequencing" who want to acquire the necessary skills to analyse scRNA-seq gene expression data.

Learning objectives

At the end of the course, participants will be able to:

• distinguish advantages and pitfalls of scRNAseq
• design their own scRNA-seq experiment
• apply a downstream analysis using R

Knowledge / competencies prerequired (Mandatory)

Participants should already have a basic knowledge in Next Generation Sequencing (NGS) techniques, or have already followed the "NGS - Quality control, Alignment, Visualisation". Knowledge in RNA sequencing is a plus. A basic knowledge of the R statistical software is required. Test your R skills with the quiz here, before registering.

Technical requirements

Please check the required installation detailed here, before the start of the course.

Program

The program of this course can be found in its dedicated GitHub page.

Application

The course is now full with a long waiting list.

The registration fees for academics are 180 CHF and 900 CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications will close once the places will be filled. Deadline for registration and free-of-charge cancellation is set to 25/09/2021. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place at the University of Bern. Please note that we comply with recent federal and cantonal recommendations, which require that participants present a COVID certificate to attend this course and wear a mask at all times. Any changes in these recommendations will be announced as soon as possible.

It will start at 9:00 and end around 17:00.

Precise information will be provided to the participants in due time.

Additional information

Coordination: Patricia Palagi

We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.