Analysis of cancer genomes using R and bioinformatic tools


23-27 January 2023


Due to the COVID-19 outbreak, this course will be held online


Course overview

Cancer research has entered a new era following the advent of en masse DNA sequencing and the availability of low cost computing power and online resources. Modern analysis of cancer genomes requires scientists to build bespoke analysis processes that can align DNA reads, extract mutational information, and leverage huge datasets.

On this course, which has been divided into five segments, you will learn how to process “raw” sequencing reads, and call the three most fundamental types of mutations found in cancer genomes: somatic single nucleotide variants, insertions and deletions, and chromosome copy aberrations. The background, theory, and main tools available will all be covered in the first part of the course. In the final segments you will learn advanced methods for sample quality control and tumour subclonal deconvolution, the task in which somatic variants are used to determine the tumour architecture (i.e., how many clones constitute the cancer) from an evolutionary perspective. Together this course will prepare any would be bioinformatician for further education or employment within a cancer research laboratory.



For the theoretical parts:

- basic understanding of biology and genomics in the context of cancer;
- basic understanding of statistics and data analysis.
Appropriate refreshers will be given within each lesson, where appropriate.

For the practical parts:
- basic knowledge of the UNIX shell processes and commands, including BASH shell scripting;
- ability to write R code with standard packages (dplyr, ggplot) and run it in RStudio.



- Proficiency beginning-to-end with a prototype cancer genomics pipeline for bulk sequencing (how to go from the sequencer outputs to somatic calls)
- Proficiency in cancer evolution analyses from bulk sequencing (how to go from somatic calls to tumour clones)
- Working knowledge of some state-of-the-art bioinformatics tools and R packages for cancer genomics



Sessions from 14:00 to 20:00 (Monday to Friday, after every 50min will be a 10min break). Sessions will follow a learn-by-practice mode. After every topic will be discussion, Q&A, and practice.

Cost overview

Package 1


480 €

Should you have any further questions, please send an email to

Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.