1. Preface

Why these tutorials?

The R2 platform (http://r2platform.com or http://r2.amc.nl) is a genomics analysis and visualization platform that tries to provide a biologist friendly interface to high throughput data. It has been developed within the department of Oncogenomics at the AMC in the Netherlands, where it still serves as a primary entry point for all types of high throughput data generated within the department. The R2 platform consists of 2 parts; a (publicly accessible) database, that stores the data, coupled to a web-interface that provides a set of tools and visualizations to mine the database.

Even though many people like the concept of R2, getting started with the platform as a new user can be a bit difficult or intimidating. With this tutorial book, we hope to get new users started and at the same time demonstrate the diverse set of functionalities to users which may already have experience with R2, but want to get familiar with new additions to the platform.

The setup of these tutorials is as follows: We have divided the different aspects of the R2 platform in a number of chapters which reflect tasks that are often performed within R2. In each chapter, step by step instructions guide you through an analysis, which you can perform online within R2 yourself. During these steps, also features related to the respective chapter, such as additional analyses or visualizations will be introduced, thereby conveying the ease of using the interconnected R2 interface.

The steps will be interspersed with additional information in Did you know boxes:

_images/R2d2_logo.pngDid you know box

These provide additional information not directly related to the tutorial steps

Chapters 2-10 demonstrate a great number of core functionalities, which you will encounter often and from different angles when working within the platform. The next set of chapters (11-18) dive more into specialized functions and in chapters 19-21 more advanced integrated analyses are shown, that some of you may be interested in. Chapters 22-24 demonstrates how users can adapt R2 to their needs by explaining how you can generate your own grouping variables or store personal lists of genes. These also explain how you can start your own user group and share information with specific other users for collaborative work. It is further elaborated how to add your own data and how to export data from R2 for use in other tools.

We hope that these tutorials will be helpful. If you have any comments or suggestions you’re welcome to contact us through the R2 website.