Bioinformatics Summer School 2019

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are familiar with omics experimental technologies and their applications in biology, have had some exposure with R, and who want to learn or expand their bioinformatics skills.

The course will cover underlying theory and practical hands-on exercises. At the end of the course, participants should be able to run analysis workflows on their own omics data, adapt and combine different tools and make informed choices about bioinformatics data analysis strategies.


  • Introduction to R and Bioconductor
  • Bioconductor core technologies
  • Elements of statistics and machine learning
  • Omics data visualisation
  • High throughput data processing
  • RNA Seq data analysis (bulk and single cell)
  • Quantitative proteomics
  • Reproducible research and workflow authoring with R markdown

Workshop faculty


  • Martin Morgan (Roswell Park Comprehensive Cancer Center, head of the Bioconductor team) - Bioconductor core technologies.
  • Laurent Gatto (de Duve Institute, UCLouvain) - R/Bioconductor, Mass spectrometry and proteomics.
  • Janick Mathys (VIB) - counts RNA-seq, differential expression analysis.
  • Lieven Clement (Statistical Genomics Group, UGent) - Statistical genomics and quantitative proteomics.
  • Charlotte Soneson (Friedrich Miescher Institute and SIB Swiss Institute of Bioinformatics) - experimental design and differential expression, and single cell RNA-seq.

Teaching assistants

Tentative schedule

Time Monday Tuesday Wednesday Thursday Friday
9.00-9.30 Registration and help desk Visualisation (with practical) Gene set enrichment analysis (with practical) Principles of differential expression analysis (experimental design and batch effect) Single cell RNA-seq
9.30-10.30 Setting the stage: bioinformatics in academic research and industry
10.30-11.00 Coffee break
11.00-12.30 Introduction to R and Bioconductor Bioconductor core technologies (SE, Genomics ranges) Practical High throughput sequencing data processing Mass spectrometry-based proteomics
12.30-14.00 Lunch (on site)
14.00-15.30 Rmarkdown for reproducible research Practical Elements of statistics and machine learning Bulk RNA-Seq Quantitative proteomics data analysis
15.30-16.00 Coffee break
16.00-17.30 Practical Working with biological annotations (with practical) Practical Practical Practical
17.30-18.00 QA and day 1 wrap-up QA and day 2 wrap-up QA and day 3 wrap-up QA and day 4 wrap-up QA and workshop wrap-up


The summer school will be limited to 50 participants.

Registration is now closed.

Given the high number of registrations received, we won't able to register any further participants.


  • Students and post-doctoral researchers: 25 euros
  • Permanent academic staff: 200 euros
  • Industry: 1000 euros


We will be offering up to 20 scholarships of up to 1000 euros (500 euros for travelling and 500 euros for accommodation) to students and early career researchers.

Course material

The course material (lectures and practicals) will be made available on the course web page.

Participants are required to bring their own laptop with the most recent release versions of R and Bioconductor installed: R-3.5.x and Bioconductor 3.6 installed. Please make sure that your computer’s hardware is sufficiently powered (>4 GB RAM, > 2 GB free disk space), that you have a working wireless card, and that you have administrator rights. Software installation instructions will be provided before the workshop and delegates are required to install all software before the workshop.

Prerequisites Participants should have had some exposure to R or have some experience with another scripting/programming language prior to the course, and feel at ease with the suggested preliminary material below.

Preliminary reading material will be offered

Accommodations and travel information

  • Participants are invited to arrange their travelling and accommodation directly.
  • Reaching Louvain-la-Neuve.

Suggested accommodations

Social programme

All participants will be invited to a dinner will be organised in the Louvain House mezzanine on Wednesday evening.

Organising committee

  • Laurent Gatto, UCLouvain
  • Jean-Baptiste Demoulin, UCLouvain
  • Axelle Loriot, UCLouvain


For inquiries related to the registration, scientific program, organisation, please contact us at


This summer school is organised in collaboration with GSK.

We would like to acknowledge financial support from GSK and thank the UCLouvain for administrative and logistic support.