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Project 3: Aggregation, Interpretation, and Visualization of Gene Fusions in Cancer #3

Open abaghela opened 6 years ago

abaghela commented 6 years ago

Aggregation, Interpretation, and Visualization of Gene Fusions in Cancer

Many cancers are defined by the presence of recurrent, subtype-defining gene fusions. While there is an abundance of informatics tools for detection of gene fusions from RNA-Seq data, these tools show little predictive overlap. Further, while annotation databases for gene fusions exist, it remains difficult to automatically annotate newly-detected gene fusions against these resources. The aim of this project is to (1) Develop methods for aggregating and comparing the results of different fusion detection tools against each other, (2) Visualizing those results in terms of fused protein domains, read evidence, and annotation status, and (3) Automatically annotating fusions for presence in selected online databases. These methods will be incorporated into a new R package and made available to the community. This project will facilitate the development of improved methods for understanding the diversity and recurrence of gene fusions, and help facilitate the clinical translation of RNA-Seq based fusion detection.

Team Lead: Rod Docking | rdocking@bcgsc.ca | @rdocking | Grad Student | BC Cancer Agency

rdocking commented 6 years ago

Hello HackSeq! I'll try to set up a base git repo with a few more details with what I'm thinking about in early September. For now, please contact me at the email above or on Twitter if you have any questions.

AndyZhuang commented 6 years ago

That is awesome ! can't wait to see the progress

rdocking commented 6 years ago

Base repo is at: https://github.com/rdocking/fusebench

hiraksarkar commented 6 years ago

Awesome!

jakelever commented 6 years ago

Hey team lead, we've been gathering Github IDs for your team members. We see that you've already started a repo for this project. So could you please add the following people as collaborators to that project?

wilcas sweetiepi eacton devanjan31 hiraksarkar stefpiatek shibuantony

Once the people are added, it'd be a great idea to start a discussion on that repo with information to get your team members started (e.g. some small suggested reading, things to look up, etc). We will also be adding everyone to Slack and creating a specific channel for each project. This may be an easier way to communicate.

We'll forward on any remaining Github IDs through this issue.

Thanks, Jake obo the Hackseq organising committee