Analyzing with RStudio Workbench Trial Version: Using R and RMarkdown

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RStudio Workbench Trial Version is now available on the UK Biobank Research Analysis Platform, allowing users to use RStudio in their analysis. This session covers everything you’ll need to know to start working with the application and use R & R Markdown on the Platform.

0:00 Introduction
2:23 Local Analysis
3:07 Cloud-based Analysis
4:29 UKB RAP Project Storage and RStudio Instance Storage
6:57 Launching RStudio Workbench Trial Version
9:51 Terminating RStudio Workbench
11:05 Overview of RStudio Workbench layout
11:23 What is dx-toolkit?
12:59 Utilize Bulk Data Files
13:57 Bulk per Sample File Folder Structure
14:24 Transfer Bulk Files/Use dxFUSE
15:57 Utilize Pheno Data
17:14 Field title vs field name vs field UK Biobank format
18:31 Table exporter inside R script
20:38 Example phenotypic data
22:57 RStudio project versus UKB RAP project
26:19 Creating RStudio project
28:51 What is renv?
30:45 Save project using dx-backup-folder
31:52 Restore project using dx-restore-folder
32:53 dx upload versus dx-backup-folder
33:55 Restoring a RStudio Project from UKB RAP Project
34:32 Install packages after restoring
35:43 UKB RAP Project Storage and RStudio Storage
38:27 Launching Studio using ttyd with Docker container
40:12 Disadvantages
42:41 Access the ttyd instance
42:57 Running Bioconductor Docker in ttyd docker run
47:27 Q&A