Analysis of single cell RNA-Seq data from 10x Genomics

Analysis of single cell RNA-Seq data from 10x Genomics

advanced bioinformatics


Start date:

29 August 2019


General context

Today it is possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). The main advantage of scRNA-seq is that the cellular resolution and the genome wide scope makes it possible to address issues that are intractable using other methods, e.g. bulk RNA-seq or single-cell RT-qPCR. These scRNA-seq datasets can be used to unravel heterogenous cell populations, for the discovery of new cell types and states, the reconstruction of developmental trajectories and fate decisions, all previously masked in bulk transcriptome analyses. However, to analyze scRNA-seq data, novel methods are required and some of the underlying assumptions for the methods developed for bulk RNA-seq experiments are no longer valid.


In this course we will discuss some of the advantages and pitfalls of scRNA-Seq and go through the whole scRNA-seq analysis pipeline. We will teach you how to do proper quality control and filtering on gene level and cell level, how to do create tSNE plots, how to get potential markers for a subset of cells ... 

Required skills

Participants should have some experience with R.  You can attend the Basic statistics in R​ training to get suffcient R background. 

The participants will be selected based on their background and a short description of the research question. We will evaluate applications and provide feedback on acceptance in the first half of July. Please use the form below to submit the required information for the selection process. Log in before you fill in the form otherwise we do not know your name and email address !

Course materials
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20-30 persons will be selected based on these texts. We will notify the participants during the first week of June.


Liesbet Martens

Liesbet Martens is a bioinformatician at the VIB-UGent Center for Inflammation Research

Contact Liesbet Martens :
Niels Vandamme

Niels Vandamme is a post-doctoral researcher at the VIB-UGent Center for Inflammation Research.

Contact Niels Vandamme :


1. Introduction

2. Overview of the pipeline

3. Analysis via R of publicly available PBMC data set

Analyze your own data or a publicly available data set of your choice under the supervision of experts

Practical info

Location & Venue

Technologiepark-Zwijnaarde 126
9052 Gent

Public transport
Public transport

Several buses drive between Gent Sint-Pieters railway station and Technologiepark: Bus 70, 71 and 72 (‘Tramstraat’)

  • Get off at the stop marked 'Bollebergen' at Grote Steenweg Noord.

  • Technologiepark is straight in front of you on the other side of the soft verge.

  • Walk into the park to the roundabout. You can see the iGent Tower on your left.

Shuttle bus

  • The shuttle service between Gent Sint-Pieters and Technologiepark runs every 15 minutes during peak hours (7.30 - 9.30 am and 4.30 - 6.30 pm).

  • The site has four stops, including one nearly in front of the iGent Tower (4th stop).

  • More info on the Tech Lane Ghent Science Park site.

Route description

You can park your car on the Tech Lane Ghent Science park in the open car parks (no barriers), like the one in front of the iGent tower across the road. These car parks have Dutch signs which read "Parkeren uitsluitend met vignet! (overtreding = wielklem)”. This means you should only park there if you have a valid car park permit. You can request such a permit by sending an email to your contact person at iGent. The permit is only valid for a single day, and will need to be placed visibly behind the car's windscreen.

Venue contact