AnVIL Demo: Epigenetics in AnVIL on September 21

AnVIL Demos
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AnVIL Demo: Epigenetics in AnVIL

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September 21, 2023 at 11:00 AM ET (your time zone) on Zoom

11:00 AM - 11:30 AM ET – Demo on AnVIL

In this demo, we’ll introduce fundamentals of epigenetic data analysis and show how you can use RStudio to look at Chip-seq experiment results on AnVIL. We’ll also briefly touch on other resources for doing epigenetics research on AnVIL.

11:30 AM - 12:00 PM ET – Q&A

We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have!

Future Demos

September 21, 2023 – Epigenetics in AnVIL

October 26, 2023 – DUOS - A tour of the AnVIL’s innovative data sharing platform, and how it can help your research

November 16, 2023 – Machine Learning with Bioconductor

December 14, 2023 – Collecting and subsetting SRA data

What are AnVIL Demos?

AnVIL Demos are a monthly, virtual meeting where we highlight what you can do on the NHGRI Analysis, Visualization, and Informatics Lab-space (AnVIL), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support.

The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3@jhu.edu). After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL.

Watch our past Demos from our YouTube playlist!

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Resources

Upcoming Events

Sign up to hear about future AnVIL Demos and announcements at lists.anvilproject.org and learn about upcoming events at AnVIL Community Events - AnVIL Portal!

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Q&A

Q: You demonstrated how to load data from GEO into RStudio on AnVIL. Where is the data when you import it into RStudio?
A: That data is stored in a temporary persistent disk, which exists as long as your virtual environment exists. This is great because you can bring in the files for a temporary exploration or analysis without having to store the data long-term. We created a graph as a result of the data analysis, so that might be something I would want to save to my workspace before I delete my environment.

Q: What kind of data can I use in AnVIL?
A: AnVIL can store any kind of datatype. You can bring in data from GEO or other public resources like we demonstrated using RStudio, or you can upload your own data in the data tab. AnVIL is has a FedRAMP Moderate security authorization, so as long as that authorization meets the protection required for your dataset you can store it in AnVIL.

Q: In the demo, you showed how to visualize the narrow peaks datatype in RStudio. Is this possible to visualize with IGV or JBrowse, have you tried loading the data to visualize them in Galaxy or other tools on AnVIL?
A: The Bioconductor trackViewer package is a little bit interactive getting to view different regions of the datasets. There is active work to get the UCSC Genome Browser into AnVIL, but other tools like JBrowse in Galaxy are available too. There are other visualizations to explore, such as a bam summary and PCA on the samples.

Q: I think you can upload a .bam file into IGV in an AnVIL workspace. Can you upload other datatypes like narrow peaks data? The datatype is a BED file.
A: According to the IGV documentation:

IGV does not currently support multiple track lines in a single BED file.