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Sunday, June 26 • 3:30pm - 6:00pm
BioinforMagic: Marrying Galaxy and Bioconductor

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Tutorial, doi: 10.7490/f1000research.1112904.1

R/Bioconductor tools are popular among bioinformaticians for conducting analyses on high-throughput genomics data. Many researchers have written and used their own R/Bioconductor tools but have limited options for sharing their methods with collaborators and ensuring reproducibility of their work. While some R/Bioconductor tools are currently integrated into Galaxy, scientific communities would benefit greatly if a larger repertoire of these tools were available. In this workshop, we will describe the key components of Galaxy tools and outline approaches for integrating R/Bioconductor tools into the Galaxy platform. Workshop attendees will engage in writing their own R/Bioconductor tool and integrating the tool into Galaxy. Additional topics covered in this workshop include wrapping R/Bioconductor tools using Planemo, dealing with R/Bioconductor dependencies, and if time permits interacting with RData objects from within Galaxy using RStudio Galaxy Interactive Environment (GIE). Participants are encouraged to bring in an R-script they want to integrate with Galaxy for the hands on session.

Prerequisites:
  • Basic understanding of Galaxy from a tool developer point of view or attendance at the Writing and Publishing Galaxy Tools workshop.
  • Basic experience with R/Bioconductor.
  • A wi-fi enabled laptop with a modern web browser.  Google Chrome, Firefox and Safari will work best. 

Instructors
avatar for Mallory Freeberg

Mallory Freeberg

Johns Hopkins University
avatar for Nitesh Turaga

Nitesh Turaga

Software Engineer, Galaxy Project, Johns Hopkins University
Galaxy



Attendees (7)