18. DataScopes

Datascopes are typically landing web-pages that provide quick jumps to (dedicated) analyses and visualizations in R2. such datascopes are frequently associated with studies that share their data, presented from a manuscript in such a way that you can repeat their analyses, but with other selection criteria etc. Another type of datascope is the ability to limit data sets to a particular selection, such as a tumor entity.

18.1. Scope

• Use data scopes to restrict data sets to a particular subject
• Use data scopes as a landing page for a specific publication / subject

18.2. Step 1: Selecting a dataset restrictive DataScope

1. DataScopes are represented in the left menu structure in R2 in the item named ‘Change Data Scopes’. Scopes can be grouped by different ‘types’ like ‘paper’ or ‘tumor type’. Depending on your account access more restricted scopes can be represented in your account. We will start by selecting a ‘dataset’ restriction Scope by clicking on ‘tumor’ > ‘neuroblastoma’. Alternatively you can click on the ‘change data scopes’ root item and get a tiled display of all the data scopes that you have access to with your account.

   

   Figure 1: Selecting a Data Scope.

2. You may have noticed that the platform now includes ‘TCGA’ in the Author column. Additionally, the number of samples available to you has greatly decreased. This is because you will now only be looking at datasets that we have a part of the TCGA consortium. This data scope can be useful if you only want to see datasets related to a specific entity that we have defined. If you want to select a new dataset, you will only be able to choose from TCGA assets. In analyses such as ‘2D distribution’, this restrictive data scope will also apply.

18.3. Step 2: Selecting a Data Scope with a landing page

1. In the first example, the DataScope did nothing more than restrict a collection of datasets at your disposal, which can be handy for quick selections. A DataScope can become much more interesting if it has also got a ‘landing page’ associated with it. These landing pages are essentially ‘quick jumps’ into the tools of the R2 platform, combined with predefined settings. The possibilities offered by the platform are nearly endless (and we are willing to create things that may not be possible yet).

2. In the next example, we will make use of a datascope that belongs to a manuscript on the analysis of 500 whole genomes of medulloblastoma (Northcott et.al. Nature 2017). Datascopes can be reached in 2 ways. Either you select ‘medulloblastoma 500’ from the ‘paper’ group in the Data Scopes menu, or you simply click on the ‘datascopes’ main menu item directly, and an overview of all the data scopes within the access of your account will become visible (and click on ‘medulloblastoma 500’).

   

   Figure 3: Datascopes overview.

3. We can go to the ‘landing page’ for this data scope by either clicking on the button ‘Goto Medulloblastoma 500 Home’ in Box 0, or click on the ‘About Medulloblastoma 500’ item near the end in the left menu.

   Figure 3: Landing Page for Medulloblastoma 500.

4. Within a landing page ‘tiles’ are defined that will quickly bring you to specific analyses and or visualizations in R2. These ‘hotlinks’ can be associated with advanced settings, and a such make the usage much easier. In the current Data Scope you can explore the genomics data for the 500 samples by investigating the annotation in the ‘cohort overview’, or check somatic mutation status in the ‘somatic variants’ tile. Another option available here is the ‘circos archive’, which enables you to dive into the events that are observed within a single patient. Most of these analyses can also be found / accessed via the main interface while very specific ones may only be provided in the scope. Here the ‘tSNE manuscript’ would be an example of the latter.

5. Another example of a recently published study is the PAN-Cancer Proteome Atlas.

Researchers have made an important contribution to the understanding and treatment of cancer by developing a Pan-Cancer Proteome Atlas (TPCPA). This research, which was conducted by an international team led by Connie Jimenez, professor of Translational OncoProteomics of Amsterdam UMC, offers a deep overview of proteins expressed in tumors of diverse forms of cancer.June 1, 2025 AUMC-website

Figure 4: Pan cancer Proteome atlas

This chapter only serves to explain the basic usage of a data scope. As you may realize, every scope can have many different options and analyses associated with it, which goes beyond what we can document here. Just have a look at the available scopes once in a while to discover what has been added, or make sure to follow our social media channels where we make announcements on this as well.

[facebook]: https://www.facebook.com/r2platform/ “FaceBook” [linkedin]: https://www.linkedin.com/company/72569174/ “LinkedIn” [X(Twitter)]: https://twitter.com/r2_platform “X(Twitter)”

Instagram

Mastodon page

18.4. Final remarks / future directions

Some of the functionalities described in this tutorial have been developed recently. If you encounter any issues or difficulties, please do not hesitate to contact R2 support at r2-support@amsterdamumc.nl. Additionally, if you have ideas for new data scopes or would like to showcase your own data in a similar way, please feel free to get in touch with us through the same support address.

We hope that this tutorial has been helpful.

Best regards,

The R2 support team.