Summer School 2024: R2 Introduction Workshop¶

Welcome¶
R2 is a publicly accessible web-based program (http://r2.amc.nl | http://r2platform.com) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. To help (bio)medical researchers get started, we offer this one day R2 Introduction Workshop.
We hope that you will find this day interesting. We would love to hear your thoughts about the workshop. We kindly ask you to fill in the following form during the workshop or at the end of the day: Evaluation Form.
Generic Workshop page
You can find the generic workshop information at http://r2platform.com/workshop
Overview of resources
The two workshop days consist each of a presentation followed by a hands-on session. Experts will be available for questions in the R2 Support Breakout Room. You can go through online step-by-step guides to do the analyses of your choice yourself and ask questions when needed.
There are two types of step-by-step guides to work through during the hands-on sessions:
- You can choose one of the courses from the left side menu to follow bigger pipelines of multiple coupled analyses to learn how to gain deeper insight into genomic data. We recommend the first course, Finding causes in Neuroblastoma genomics data , that follows the same research line as was performed in a Nature article in 2017.
- You can choose a topic in the Online Tutorial to follow smaller guides about specific analyses of your interest. Please find an overview of the guides per topic of the presentation at the page From presentation to your own analysis. You can find the complete online R2 tutorial here.
Copyright (c) 2006-2024 Jan Koster
Table of Contents
R2 Introduction Workshop
Basics Courses
Additional Course Material
- 1. Molecular Oncology - R2 Practical - Colorectal Cancer
- 1.1. Introduction
- 1.2. Normal colonic epithelium vs adenomatous tissue: a first impression of genomic data
- 1.3. Identifying groups and their characteristics: CMS
- 1.4. A song of Genomic Alterations en Oncogenes
- 1.5. Therapeutic: Effects of imatinib: shifts of signature profiles and molecular subtypes
- 1.6. Identifying key drivers of CRC: superenhancers controlling gene expression
- 1.7. Summary
- 1.8. Evaluation
- 1.9. Final remarks / future directions
- 2. Differential gene expression in micro-array colon cancer data