R2 Training Programme

Welcome

R2 is a publicly accessible web-based program (https://r2.amc.nl | https://r2platform.com) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. To help (bio)medical researchers get started, R2 offers a variety of online educational resources that you can find below.

Overview of resources

R2 offers a variety of resources to help you deepen your understanding of the platform and of genomics research in general. Below, we’ve listed several of these resources:

• In the navigation bar on the left, you can find several courses that are designed to introduce you to basic R2 analysis pipelines. The pipelines consist of multiple coupled analyses to learn how to gain deeper insight into genomic data. We recommend the Basic Courses, Molecular Oncology - R2 Practical - Colorectal Cancer and Finding causes in Neuroblastoma genomics data. The additional course material has not been updated with recent changes on the platform’s interface.
• You can check out the Online R2 Tutorial that provides many smaller step-by-step guides of R2 analyses.
• Check out the Datascope page, where clickable tiles allow you to navigate interesting resources and enter R2 result pages with preset analysis settings. Note that these result pages are interactive, such that you can simply continue your research from any of these pages.
• Past workshop material can be found on this R2 Introduction Workshop page

If you would like to use R2 for your research in the future, then just visit https://r2.amc.nl and get started. You can contact the R2 Support Team with questions about your own research and public or private data set uploads (with public or restricted access).

If you encounter discrepancies between the instructions in this course and the R2 platform options, please let our R2 Support Team know. We continuously enhance the platform by adding new functionalities and refining existing features. As a result, our documentation and course instructions may occasionally fall behind. We very much appreciate your feedback!

Copyright (c) 2006-2025 Jan Koster

Basics Courses (Recommended)

• 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. (OPTIONAL) Identifying key drivers of CRC: superenhancers controlling gene expression
  • 1.7. Evaluation
  • 1.8. Final remarks / future directions
• 2. Finding causes in Neuroblastoma genomics data
  • 2.1. Introduction
  • 2.2. Finding prognostic factors in your data
  • 2.3. Different expression patterns between subgroups and the underlying biology
  • 2.4. Answers
  • 2.5. Other options to explore R2
• 3. Clinical Cell biology – Vitiligo training course
  • 3.1. Introduction
  • 3.2. Selecting a dataset
  • 3.3. Pathogenesis of vitiligo
  • 3.4. Finding differentially expressed genes.
  • 3.5. Analyze differential expression using Gene sets
  • 3.6. Analyzing differential expression using Gene signatures
  • 3.7. Looking for T-cells in the vitiligo dataset from Passeron
  • 3.8. Studying vitiligo on a cellular level using single-cell RNAseq
  • 3.9. Melanoma
  • 3.10. Note!!!

Additional Courses (NOT UP-TO-DATE)

• 1. Investigating structural variants
  • 1.1. Exploring the dataset
  • 1.2. Pie Charts
  • 1.3. Somatic mutations in neuroblastoma
  • 1.4. Further use of WGS data; structural variants
  • 1.5. Chromothripsis
  • 1.6. Locations of structural variants, hotspots?
  • 1.7. Remarks
• 2. Gene expression in Rheumatoid Arthritis
  • 2.1. Immune response in blood and synovial fluid
  • 2.2. Effects of treatment
  • 2.3. Final remarks / future directions
• 3. Differential gene expression in micro-array colon cancer data
  • 3.1. Introduction
  • 3.2. First Part: Colon versus Normal tissue
  • 3.3. Second Part: MSI in Colon tumors.