Creating a User-defined Endpoint(s)
The FinnGen core analysis provides endpoints that cover all branches of the ICD tree. However, there might be specific additional endpoints you are interested in or different definitions of existing endpoints.
We provide a variety of tools you can use to make your own user-defined endpoints. Red data (individual-level data) rights are needed to have access to the tools and data. For more about red data see "What do we mean by "red" and "green" data?", "Do I need "red" or "green" data access?", and "If I already have green data access, how do I apply for red?".
An example workflow may help to choose between the tools, plan your own workflow, and get started with endpoint defining. For instructions of the most common analyses researchers are conducting with FinnGen data in FinnGen Sandbox see General workflows for the most common analyses.
Tools for creating and visualizing a user-defined Endpoint(s) (Tools usage needs red data access).
| Tool | Description | GUI tool | coding skills needed |
|---|---|---|---|
Creating user-defined cohorts and visualization | Yes | No | |
Examine & export variant-level information | Yes | No | |
Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization | Yes | No | |
Visualize large numbers of longitudinal cases with glyphs of user-defined conditions, export | Yes | No | |
Interactive coding using R language | No | Yes | |
Jupyter (Python) | Interactive coding using Python language | No | Yes |
BigQuery connections using R and Python language | No | Yes |
For more tools available in the Sandbox see Which tools are available.
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