Try out RStudio in Terra

Just a few hours ago, the rstudio::global(2021) conference completed a full 24 hours of really cool talks, which was all the more impressive for being a completely free event. 

So we thought, what better way to keep the party going than to share a video showing how to use RStudio in Terra?

Yes, you read that right, RStudio is available in Terra. Specifically, we provide a cloud environment pre-configured to run the server version of RStudio, as an alternative (or complement) to Jupyter Notebooks. It’s an alpha feature, which means it’s still under active development and isn’t fully documented yet, but I’ve been kicking the tires all week so I thought I’d show you a real-world example of how it works.

This 7-minute video shows you how to select the right cloud environment for running RStudio, import some data and get started with Bioconductor packages for single-cell RNA-seq analysis. All of the steps shown here can be reproduced with publicly available resources; see the list at the end of this post.

If the resolution doesn’t look right when viewing in full screen, click the YouTube logo in the lower right corner of the player to go watch the video in its original format on YouTube.

The RStudio integration in Terra is the product of a great collaboration with the Bioconductor team as part of the AnVIL project, which had already produced a preconfigured environment for using Bioconductor in Jupyter Notebooks (which you can try out by following the instructions in the public Bioconductor workspace). 

In parallel, and also as part of the AnVIL project, we’ve been working with the Galaxy team — so there might be a sneak preview of Galaxy in Terra in our collective future as well. Make sure to subscribe to this blog and/or the Terra channel on YouTube to be notified when we upload new content.

 


Resources and further reading

Public Terra workspaces

Bioconductor workspace

HCA_Optimus workspace

Documentation

Getting started with Terra (for newcomers)

AnVIL project on Github: AnVIL, RStudio and Bioconductor

Bioconductor: AnVIL package docs

Bioconductor: SingleCellExperiment intro docs

Optimus Pipeline FAQs

Literature

Amezquita R, Lun A, Becht E, Carey V, Carpp L, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pages H, Smith M, Huber W, Morgan M, Gottardo R, Hicks S (2020). “Orchestrating single-cell analysis with Bioconductor.” Nature Methods, 17, 137–145. https://www.nature.com/articles/s41592-019-0654-x.

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