Complete end-to-end guides¶
The GEL RE offers huge possibilities for analysing and exploring genomic and phenotypic data. This documentation can guide you through it but there is a lot of information here, which can be a bit overwhelming when you first get started.
Here are a few common use-cases. Each links out to another page which will provide a rough guide to the tools in the RE you might want to use to complete your task and some further reading in the documentation to help you along.
For some there are examples of how you can complete these tasks using either no code tools or programmatic and command-line tools. Be aware that there is a limit to the scale of the analyses you can do with no code tools.
- I'm interested in a phenotype and I want to know what variants are related
- I'm interested in a gene and I want to know what phenotypes are related
- I want to know more about pathogenicity of different variant types on a large scale
- I want to find a diagnosis for patients who didn't get one through primary clinical interpretation
How to use these pages
On some of the the tutorial pages you can switch between categories including no code, pre-run analyses, existing tools and from scratch. Please select the version that matches your skills and the scale of the task you want to do.
| Category | Scale | Skills needed | Overview | Audience |
|---|---|---|---|---|
| no code | small | basic IT skills | Uses no code tools in the RE | Clinicians and biologists without coding or command line skills |
| pre-run algorithms | small | basic IT skills | uses data generated in-house | Clinicians and biologists without coding or command line skills |
| existing tools | large | command line and limited coding | uses pipelines generated in-house to carry out standardised analyses | bioinformaticians/computational biologists doing standard analyses |
| from scratch | large | command line, coding and common bioinformatics tools | illustrates the steps you might follow using common bioinformatics tools to carry out custom analyses | bioinformaticians/computational biologists doing custom analyses |
The instructions in each section include links to the relevant pages in the documentation. Links are tagged as:
- Tutorials
- Tools - descriptive
- Data - descriptive
- Pre-made workflows
- Reference lists/tables
Get a tutorial on your task¶
If your task is not listed here and you'd like to see a tutorial on how to do it, please contact us via our Service desk portal and let us know what it is you want to do in the RE, stating that this is a "tutorial request".