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Working with R in the Research Environment, March 2025¶
R is a powerful programming language with numerous libraries for biological data analysis and visualisation. Within the Genomics England Research Environment, you have access to many versions of R and associated libraries, along with Rstudio for interactive analysis. The High Performance Cluster allows you to run analyses with significant compute.
In this training session, you will learn how to work in Rstudio in the Research Environment, to run your R scripts on the HPC, and to access the R libraries within the Research Environment, which may be different to how you are used to working outside the Research Environment. You will also learn how to access clinical data with R.
Timetable¶
13.30 Welcome and introduction
13.35 Working with RStudio on the HPC
13.45 Plotting in R
13.55 Find out what R libraries are available for different versions of R
14.15 Query clinical data with R
14.45 Getting help and questions
Learning objectives¶
After this training you will know:
- How to use Rstudio on the High Performance Cluster
- How to use R libraries in the Research Environment
- How to query Genomics England clinical data with R
Target audience¶
This training is aimed at researchers who:
- Are working in the Genomics England Research Environment
- Can programme in R
Date¶
11th March 2025
Materials¶
You can access the redacted slides and video below. All sensitive data has been censored.
Slides¶
Download the slides Download the slides
Video¶
Give us feedback on this tutorial
Code¶
Give us feedback on this tutorial
You can find the Rstudio project and scripts used inside the RE in:
/gel_data_resources/example_scripts/workshop_scripts/working_with_r_2025
Q&A¶
Q&A
Do I need to login to RE for this training
live answered
There was a link previously on the screen for these instructions, please could you re-share in chat? Thx
https://re-docs.genomicsengland.co.uk/enable_rstudio/
do we need to login into HPC before ?
live answered
Is there any advantage between RStudio and Jupyter for working with R in the Gel RE?
live answered
do we need clouOS account before access in RE
Yes, you will need to sign up for CloduOS. We’ll be sending out an email after the session which includes instructions on how to get access.
Is there a difference between NHSE data in GMS and main programe?
live answered
sorry whre was the data schema for nhs england sets?
live answered
are there any drugs data?
live answered
Is the same types of data but are the patients actually different? Is there a way to understand how many patients are duplicate records?
live answered
can we access genomic data in R/Python (e.g., BAM and VCF) for downstream processing
https://re-docs.genomicsengland.co.uk/rd_cohorts/#filepaths