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.
  • Koen Van den Berge (Statistical Genomics Group, UGent) - Single cell RNA-seq.
  • Oliver Crook (University of Cambridge, UK) - Statistics and machine learn.

Teaching assistants

  • Members of the UCLouvain Computational Biology research group.
  • Members of the SMCS (Support en Méthodologie et Calcul Statistique) platform.
  • Jérôme Ambroise, CTMA, IREC, UCLouvain.
  • Alexander Botzki, Elixir, VIB, Gent.


Time Monday Tuesday Wednesday Thursday Friday
8.30-9.00 Coffee and breakfast (on site)
9.00-9.30 Registration, help desk and opening remarks (slides) Bioconductor core technologies (SE, Genomics ranges) (Rmd, html) (MM) Gene set enrichment analysis (with practical) (slides pdf, html, Rmd) (MM) High throughput sequencing data processing (slides) (CS, JM) Single cell RNA-seq slides (KVB)
9.30-10.30 Talk: Bioinformatics at GSK Vaccines, Christophe Lambert
10.30-11.00 Coffee break
11.00-12.30 Introduction to R and Bioconductor (Rmd, html) (MM) Visualisation (html (part 1) and slides (part 2) (LG) Elements of statistics and machine learning (slides) (OC) Practical: RNASeq (Rmd and html) Mass spectrometry-based proteomics (slides, vignette Rmd html) (LG)
12.30-14.00 Lunch (on site)
14.00-15.30 Rmarkdown for reproducible research (slides) (LG) Practical: Bioc core technologies (Rmd, html) Practical: stats/ML (Rmd and html) (OC) Bulk RNA-Seq (slides) (CS, JM) Quantitative proteomics data analysis (slides and practical) (LC)
15.30-16.00 Coffee break
16.00-17.30 Practical: R/Bioconductor and Rmarkdown (Rmd, html) Working with biological annotations (Rmd, html) (MM) Principles of differential expression analysis (experimental design and batch effect) (slides) (CS) Practical: RNASeq (Rmd and html) Practical: proteomics
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



Registrations are now closed.


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


We are happy to offer 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-3.6.x and Bioconductor 3.9 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. Please follow these software installation instructions 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 by Martin Morgan below.

Accommodations and travel information

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

Suggested accommodations

Social programme

All participants are invited to join for dinner in the Louvain House mezzanine on Wednesday at 7pm.

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

Code of conduct

This code of conduct is developed based on the Bioc2019 conference code of conduct.

BSS2019 is dedicated to providing a supportive, collegial, and harassment-free experience for everyone, regardless of:

  • gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion.
  • intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.

We do not tolerate harassment, intimidation, or bullying of participants in talks, workshops, poster sessions, social activities, or online. Sexual language and imagery is not appropriate. Participants violating these rules may be sanctioned or expelled from the event with no refund, at the discretion of the organisers.

Examples of unacceptable harassment, intimidation, and bullying behaviour

Harassment includes, but is not limited to:

  • Making comments, to an audience or personally, that belittle or demean another person
  • Sexual images in public spaces
  • Stalking or following
  • Harassing photography or recording
  • Sustained disruption of talks or other events
  • Inappropriate physical contact
  • Unwelcome sexual attention
  • Advocating for, or encouraging, any of the above behaviour

Intimidation and bullying include, but are not limited to:

  • Aggressive or browbeating behaviour directed at someone during a public presentation
  • Mocking or insulting another person’s intellect, work, perspective, or question/comment
  • Making reference to someone’s gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age, religion, or other personal attribute in the context of a scientific discussion
  • Deliberately making someone feel unwelcome


Participants asked to stop any harassing behaviour are expected to comply immediately.

If a participant engages in harassing behaviour, event organisers retain the right to take any actions to keep the event a welcoming environment for all participants. This includes warning the offender or expulsion from the event with no refund.

Event organisers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants.

We expect participants to follow these rules at all event venues and event-related social activities. We think people should follow these rules outside event activities too! Reporting

If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible. Harassment and other code of conduct violations reduce the value of our event for everyone. We want you to be happy at our event. People like you make our event a better place.

Personal Report

You can make a personal report with Laurent Gatto or Axelle Loriot. You can contact them directly or by email at ``.

When taking a personal report, our staff will ensure you are safe and cannot be overheard. They may involve other event staff to ensure your report is managed properly. Once safe, we’ll ask you to tell us about what happened. This can be upsetting, but we’ll handle it as respectfully as possible, and you can bring someone to support you. You won’t be asked to confront anyone and we won’t tell anyone who you are.

We value your attendance.


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.